fix bugs
 

 Version bump to v2.13.1
 

 add .positai to .Rbuildignore and .gitignore
 

 add figures for README.md
 

 version bump 2.45.1
 

 deprecate twoWayAlphabetFrequency() and twoWayAlphabetFrequencyByQuality()
 

 Add missing fnd entries to Authors@R in DESCRIPTION
 

 Add missing fnd entries to Authors@R in DESCRIPTION
 

 Uncommitted changes from Tuomas Borman PR #314
 

 Add missing fnd entries to Authors@R in DESCRIPTION 

 version bump 1.29.1
 

 Biostrings 2.81.1: Formally deprecate the scoring matrices

All the BLOSUM* and PAM* scoring matrices are now located in the pwalign
package (since BioC 3.20). Starting with BioC 3.24, the scoring matrices
located in the Biostrings package are formally deprecated and will soon
be removed from the package.
 

 Add missing fnd entries to Authors@R in DESCRIPTION
 

 version bump 1.51.1
 

 chore: modernize package to current Bioconductor standards

- Updated DESCRIPTION (version bump, R >= 4.6.0, standard biocViews)
- Migrated legacy inst/CITATION to bibentry() format
- Consolidated inst/NEWS into top-level NEWS.md
- Cleared out explicit regex export in NAMESPACE to pass BiocCheck

Co-authored-by: Gemini Code Assist <gemini@google.com>
 

 Migrate pr_check.yml to ci.yml (#4)

* Add ci.yml reusable-workflow wrapper

* Remove pr_check.yml (replaced by ci.yml) 

 CI: Maybe parallel tests cause covr::package_coverage() hang
 

 CI: GitHub actions need the "remotes" package
 

 Add missing fnd entries to Authors@R in DESCRIPTION (#1)
 

 Add missing fnd entries to Authors@R in DESCRIPTION 

 move Date close to Version in DESCRIPTION
 

 Add missing fnd entries to Authors@R in DESCRIPTION 

 Add ci.yml reusable-workflow wrapper 

 Add missing fnd entries to Authors@R in DESCRIPTION 

 docs: add AGENTS.md instructions for AI assistants
 

 docs: add AGENTS.md instructions for AI assistants
 

 docs: add NEWS entry for Bioconductor 3.23 sync version bump
 

 Merge pull request #99 from gladkia/98-support-custom-track-options

98 support custom track options 

 test: improve Shiny tests
 

 chore: clean up
 

 Merge branch 'master' into 98-support-custom-track-options
 

 chore: bump v+c
 

 build: update R version in GA workflows
 

 chore: update as suggested by the reviewer
 

 test: make linter happy
 

 doc: update docs
 

 feat: add support for additional track options (on the js level)
 

 Merge branch 'devel'
 

 docs: add NEWS entry for Bioconductor 3.23 sync version bump
 

 Merge pull request #41 from gladkia/40-compatibility-of-igvr-with-cram-files

Add CRAM file support via new CramTrack class (fixes #40) 

 doc: update docs
 

 Merge pull request #38 from gladkia/bioc_sync

Bioc sync 

 Merge pull request #35 from gladkia/server_migration

Server migration 

 feat: use VCF subset file for ampad/NIA-1898/chr22
 

 feat: change file links from igv-data.systemsbiology.netm to gladki.pl/igvR
 

 Resolve conflict in DESCRIPTION - using Bioconductor devel version 2.35.0
 

 Merge branch 'devel' into bioc_sync
 

 doc: add examples
 

 chore: improve DESCRIPTION
 

 build: add initial GHA generated with biocthis
 

 Lift test coverage from ~84% to ~92%

Adds 7 new test files and expands 4 existing ones, raising overall
package coverage well above the 90% target. No production code was
deleted or its functionality reduced — every uncovered branch was
addressed by exercising it from a new test.

Coverage measured locally with covr::package_coverage() against tracked
files in R/. Full test suite: 370 PASS, 0 FAIL, 13 WARN, 4 SKIP.

New test files:
- test-check_species_babelgene.R: 4 invariant branches (target=human +
  source not in dict, source=human + target not in dict, neither human,
  valid pair)
- test-check_agg_args.R: 6 cases covering happy path, agg_fun cleared
  for non-matrix gene_df / non-rownames gene_input, gene_output coerced
  to "rownames", return_args=FALSE flag, no-aggregation passthrough
- test-map_orthologs_gprofiler.R: NULL/empty/NA-only inputs, same
  source/target short-circuit, chunk_size validation, non-chunked path,
  chunked-serial path with multi-chunk, chunked-parallel (PSOCK) path
- test-helpers.R: invariants for check_keep_popular, check_sparseMatrix,
  non121_strategy_opts (full dict / synonyms / errors / include_agg),
  is_human, is_matrix/is_sparse_matrix, is_converted, check_bool_args
  (5 per-arg branches), invert_dictionary, methods_opts,
  gene_input_opts/gene_output_opts, check_agg_opts
- test-internal-helpers.R: check_gene_map, check_agg_opts, filter_gene_df
  (rownames/colnames/error), use_cache (NULL save_dir + cached file),
  check_gene_df_type (data.table conversion + error), aggregate_rows
  (unknown method error), map_orthologs (unknown method error),
  all_genes (unknown method fallback), many2many_rows
  (aggregate_orthologs=FALSE), get_orgdb_gprofiler (use_local TRUE/FALSE)
- test-run_benchmark_once.R: run_convert_orthologs=FALSE branch, cache
  hit on second call, within-species (is_human) path
- test-misc-helpers.R: is_gha (env var present/absent), load_rda, rotate_clades
  (matching/non-matching tip sets), aggregate_rows_monocle3 (mean +
  count), get_cache_save_path uniqueness, cache_dir, messager,
  format_species, all_species, add_rowcol_names (rownames + colnames),
  check_gene_output, gconvert_target_opts (validates target for known
  species)

Expanded test files:
- test-prepare_tree.R: local-newick else-branch, force_ultrametric=FALSE,
  age_max calibration
- test-aggregate_mapped_genes.R: transpose=TRUE, within-species map_genes
  branch, sort_rows=TRUE, as_integers=TRUE, early-exit rename-only path
- test-infer_species.R: test_species=NULL default, method-as-test_species
  expansion, make_plot=FALSE
- test-create_background.R: use_intersect=FALSE (union), user-supplied bg,
  same-species fast path with as_output_species=TRUE

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 

 version bump 1.1.1
 

 Bump version
 

 Mention s3_client new default value in NEWS
 

 Version 2.1.1: align vignette YAML with DESCRIPTION; exclude venv from builds

- Bump patch after BioC 3.23 sync metadata
- Set vignette version fields to match package version
- Add venv to .Rbuildignore
- Fix NEWS bumpversion search template for top section header

Made-with: Cursor
 

 Fix test-map_genes: message() escapes tryCatch under testthat

Same bug pattern as the previous fix in run_benchmark_once.R (commit
dad4348). The planarian (Schmidtea mediterranea) test wraps
`map_genes(species = "Schmidtea mediterranea")` in tryCatch because the
planosphere mapping file is downloaded at runtime and may fail (e.g. the
Windows runner under R 4.6 can't resolve the cache path —
"smed_20140614.mapping.rosettastone.2020.txt.gz does not exist or is
non-readable"). The handler did `message(e); NULL`, but `message()`
re-signals condition objects, and testthat's calling handlers treat the
re-signaled error as a test failure — escaping the tryCatch.

Fix: pass `conditionMessage(e)` (a plain string) to `message()` so the
text is printed without re-signaling. The test still gracefully skips
the assertion when the download fails, which is the intended behaviour.

Surfaced by run 25110211328 on Windows; macOS passed because the
download succeeded there.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: Rarr

      Commit: fb29fc1c8232dccaea37a6800f41530adc774dd4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 15:30:33 +0200

      Commit message:


	  
		
 Run devtools::document()
 
    
  
    

      Package: Rarr

      Commit: e505b1f79c5a8815162f4edf1295d67788b72c37

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 14:24:47 +0200

      Commit message:


	  
		
 Wrap linter in requireNamespace()
 
    
  
    

      Package: Rarr

      Commit: 273563a9dedb23a0ccd4af7c5773da14034c48dc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 13:50:05 +0200

      Commit message:


	  
		
 Save snapshot
 
    
  
    

      Package: Rarr

      Commit: a83111088f106507a7423ab86c00b31d16f1d431

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 12:32:21 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: 7b4a10a994d91816fb9953d8e17b17f0bfdcccfa

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 12:31:57 +0200

      Commit message:


	  
		
 Mention zarr v3 on s3 fix
 
    
  
    

      Package: Rarr

      Commit: 118d0c62133ad0236c4fa2dd58012ed4906a912c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 12:27:41 +0200

      Commit message:


	  
		
 Add custom linter to ensure fromJSON always has simplifyVector = FALSE
 
    
  
    

      Package: Rarr

      Commit: f99b4359045f3da0eb2e3b81c22092d1d671bcfa

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 12:20:32 +0200

      Commit message:


	  
		
 Add test for s3 metadata bug
 
    
  
    

      Package: Rarr

      Commit: 786fa4e5ba6a9b42eecce7ada98f93e1bcc2372b

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2026-04-28 21:57:30 +0200

      Commit message:


	  
		
 simplifyVector=FALSE whenever fromJSON is called
 
    
  
    

      Package: Rarr

      Commit: f0c9673bd345bd6d76ed97bfa9c96ac9bd4fb24f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 11:18:44 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: a3573a0eb4b235a399a372a01b85c988c5ff1fbc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 11:18:14 +0200

      Commit message:


	  
		
 Mention vlen-utf8 performance improvement in NEWS
 
    
  
    

      Package: Rarr

      Commit: 0fe2f45c07f68bc403c5f8fcd5303166c423a629

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-22 11:18:33 +0200

      Commit message:


	  
		
 Run only vlen-utf8 benchmark
 
    
  
    

      Package: Rarr

      Commit: 4216c8f4efe7ecf3d5d92d95f2457cc917267cbd

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-22 11:15:11 +0200

      Commit message:


	  
		
 Convert vlen_utf8 decode codec in C
 
    
  
    

      Package: Rega

      Commit: 6ca901a186bcaa6e37c8fa82081910ba502c49a6

      Author:  Igor Cervenka <wormikk@gmail.com> 

      Date: 2026-04-29 14:57:30 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'bioc/devel' into devel
 
    
  
    

      Package: Rega

      Commit: b33cc16edf798181c760454d9a9d3e3c1f0c53e0

      Author:  Igor Cervenka <wormikk@gmail.com> 

      Date: 2026-04-29 14:53:54 +0200

      Commit message:


	  
		
 Fix samples_in_db return value
 
    
  
    

      Package: orthogene

      Commit: 253239d9f2ffea5bb2905066f511106154c03b81

      Author:  bschilder <brian_schilder@alumni.brown.edu> 

      Date: 2026-04-29 08:57:47 -0400

      Commit message:


	  
		
 Revert g:Profiler workarounds — upstream API regression is fixed

g:Profiler confirmed and fixed the API regression that returned literal
`NaN` in JSON. Unmatched genes are once again returned as `"N/A"`. The
tests that failed during the Bioc 3.23 freeze were correctly catching
that regression — masking them was the wrong long-term call.

Revert from 1.17.3:
* Examples for `convert_orthologs()`, `map_orthologs()`, `all_genes()`
  no longer pass `method = "homologene"`; they exercise the default
  (g:Profiler-first) path again.
* Tests in `test-aggregate_mapped_genes`, `test-convert_orthologs`,
  `test-infer_species` no longer pin `method = "homologene"` on calls
  that should be testing the default behaviour.
* `test-all_genes_gprofiler` and the `method = 'gprofiler'` block in
  `test-convert_orthologs` no longer wrap calls in tryCatch+skip — the
  whole point of those tests is to fail loudly when g:Profiler breaks.
* `test-run_benchmark` no longer uses `na.rm = TRUE` in the aggregate
  mean checks — NA from a backend means *something is wrong* and we
  want the assertion to surface it.

Kept:
* `run_benchmark_once()` still uses `message(conditionMessage(e))`
  inside its tryCatch error handlers — `message()` re-signals
  the condition and escapes tryCatch under testthat. Unrelated to
  g:Profiler.
* `test-infer_species` still tolerates ties in `top_match` — when human
  and monkey tie at the same `percent_match` via babelgene, the test
  passes as long as the expected species is among the ties.

Bumps to 1.19.1 on top of the post-3.23 devel-cycle bump (1.19.0).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: BioNAR

      Commit: 5acd4d1e61c1fd9129eca169c68fdd6097b60a72

      Author:  Anatoly Sorokin <lptolik@gmail.com> 

      Date: 2026-04-29 12:47:06 +0100

      Commit message:


	  
		
 Merge commit '2a185b929475492134236fa44eddc37b03434864' into devel
 
    
  
    

      Package: BioNAR

      Commit: 7254b80793e762bafa709f9c79f35d6ed7cc5009

      Author:  Anatoly Sorokin <lptolik@gmail.com> 

      Date: 2026-04-29 12:41:18 +0100

      Commit message:


	  
		
 fix a bug in clusterOra when not "name" used as vertex ID
 
    
  
    

      Package: OmnipathR

      Commit: 3e1139172d3036ffd772ebb945bc5e338ac63fde

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-04-29 12:26:56 +0200

      Commit message:


	  
		
 propagate bioc version bump to bump2version
 
    
  
    

      Package: asuri

      Commit: dfe8e2e9b229ff3540d19c28ed0b5e9e5e95bc31

      Author:  aberral <aberralgonzalez@gmail.com> 

      Date: 2026-04-29 11:38:45 +0200

      Commit message:


	  
		
 Version Fix
 
    
  
    

      Package: asuri

      Commit: 552a9392ac125ffb7a1ea1186c237777f8a40cbd

      Author:  aberral <aberralgonzalez@gmail.com> 

      Date: 2026-04-29 11:37:58 +0200

      Commit message:


	  
		
 "Resolve conflict: accept Bioconductor devel version 1.1.0"

Merge remote-tracking branch 'upstream/devel'

# Conflicts:
#	DESCRIPTION
 
    
  
    

      Package: asuri

      Commit: 6255c29816ea84592365802f1017ddb4ea3b1aa7

      Author:  aberral <aberralgonzalez@gmail.com> 

      Date: 2026-04-29 11:35:09 +0200

      Commit message:


	  
		
 1 version
 
    
  
    

      Package: asuri

      Commit: a6f0d65a123ffcd70715a67f5c55505de46f30db

      Author:  aberral <aberralgonzalez@gmail.com> 

      Date: 2026-04-29 11:32:11 +0200

      Commit message:


	  
		
 update version for devel cycle
 
    
  
    

      Package: scater

      Commit: 8c547447c1451ed6fd95c341cd777e12cee9a439

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2026-04-29 10:22:09 +0100

      Commit message:


	  
		
 Merge branch 'devel' of git.bioconductor.org:packages/scater into devel
 
    
  
    

      Package: scater

      Commit: 15c18a1f15e968af3a752bd22c4ea8c32db3107d

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2026-04-29 10:21:42 +0100

      Commit message:


	  
		
 Resolve #227
 
    
  
    

      Package: scater

      Commit: a55ac0dbcbfe489826f0b7ce053ca8cb4a7af676

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2026-04-07 10:41:52 +0100

      Commit message:


	  
		
 Merge pull request #226 from alanocallaghan/minor-fix

Make identities of summarized columns are more obviously correct. 
    
  
    

      Package: scater

      Commit: 46c70c3395dc86de5e25977eaf1bd5e3b81be395

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-04-07 12:50:00 +1000

      Commit message:


	  
		
 Make identities of summarized columns are more obviously correct.

It was actually correct already but the correctness was hard to prove; now it
should be obvious that the columns of the summarized matrix match up to the
rows of the dataframe containing the group + block identities.
 
    
  
    

      Package: Rarr

      Commit: db556a97ed34169fb4777368a0723c110628d1c7

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 10:56:04 +0200

      Commit message:


	  
		
 Revert touchstone to release
 
    
  
    

      Package: Rarr

      Commit: 019187b20ab44d566c35d507bea8a3ab796a9dc2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 10:29:15 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: c3d3c3e3a48a59e825f275877161e3167eeb1c9a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 10:29:07 +0200

      Commit message:


	  
		
 Mention new blosc options and vlen fix in NEWS
 
    
  
    

      Package: Rarr

      Commit: f353c3d50e82bc63b5d7033f423cd183fed405cc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-24 16:53:15 +0200

      Commit message:


	  
		
 Record blosc typesize in metadata
 
    
  
    

      Package: Rarr

      Commit: 23cc748b3ffc0b2d4439c85f0823e19d37351466

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-24 17:08:35 +0200

      Commit message:


	  
		
 Add test for blosc vlen compression
 
    
  
    

      Package: Rarr

      Commit: 2794f426cf12f1e34cca7e3f8ebc9e53c53ba434

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-24 16:20:26 +0200

      Commit message:


	  
		
 Convert blosc compression to a codec
 
    
  
    

      Package: Rarr

      Commit: 352079166e5bb81e13ec7a58d030b218caa9aa65

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-21 20:18:05 +0100

      Commit message:


	  
		
 Snapshot test .zarray blosc
 
    
  
    

      Package: Rarr

      Commit: 59f269649b73cfc5986b5d2cc130543a49cc5a7b

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-21 14:54:55 +0100

      Commit message:


	  
		
 Test more complex blosc options
 
    
  
    

      Package: Rarr

      Commit: 4dd4a21e07af1f8495da2549a512c54cff63bdeb

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-20 20:02:02 +0100

      Commit message:


	  
		
 Write shufflemode as text in metadata
 
    
  
    

      Package: Rarr

      Commit: 02bd78dde108b84d7c3651041c69cc8b7e9b1567

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-20 19:42:12 +0100

      Commit message:


	  
		
 Use requested blosc opts from R code
 
    
  
    

      Package: Rarr

      Commit: edf61e84dba3fe2e2be5071898e494eab550a133

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-20 19:17:13 +0100

      Commit message:


	  
		
 Add config options to use_blosc()
 
    
  
    

      Package: Rarr

      Commit: c070483d9907f1b22e8d4a6b5d85b748e93bf1b1

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-18 15:31:40 +0100

      Commit message:


	  
		
 Add more options to blosc c function
 
    
  
    

      Package: Rarr

      Commit: f9fccacafe13251f6fff107ad4bee969ebb7c868

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-29 10:34:55 +0200

      Commit message:


	  
		
 Fix lintr config
 
    
  
    

      Package: Rarr

      Commit: 07cb75dacf7ba488007446e70e7690dc64d9241c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 18:41:31 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: 4a941c204cae9e796609c8ebacab9ecaf8f715fc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-14 18:59:04 +0200

      Commit message:


	  
		
 Mention empty chunks change in NEWS
 
    
  
    

      Package: Rarr

      Commit: 68acda1157d865a6af8c435c4a217c43e0940da2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-14 18:57:23 +0200

      Commit message:


	  
		
 Add test for not writing empty chunks
 
    
  
    

      Package: Rarr

      Commit: 3c5bad5b1586acc39f3eb25e9bfd7e4b4df239a7

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-14 11:08:02 +0200

      Commit message:


	  
		
 Skip writing empty chunks
 
    
  
    

      Package: Rarr

      Commit: 488169c1098c157ae3140a4e1ee687c69ca46f2a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 17:46:56 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: Rarr

      Commit: 65352e8f221813bb7091131433cbfe624dab7b12

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 17:46:28 +0200

      Commit message:


	  
		
 Mention normalize_array_path() speedup in NEWS
 
    
  
    

      Package: Rarr

      Commit: 93e8666232f68fe12830a2d41a75d08fcabd018f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 17:42:11 +0200

      Commit message:


	  
		
 Use a single regex to extract region, bucket and object
 
    
  
    

      Package: Rarr

      Commit: 3764df97f31d55655cb0a994d7c477953f57d2f5

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-22 16:23:08 +0200

      Commit message:


	  
		
 Convert repeated gsub() to regmatches()
 
    
  
    

      Package: Rarr

      Commit: 5ad1e34f99d778d4d82be8166313d66f7a4e11cc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-22 16:22:20 +0200

      Commit message:


	  
		
 Use startsWith() to avoid complex regex
 
    
  
    

      Package: Rarr

      Commit: 1e384352f77f55ec5efccabd0f78116e05b5e686

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-22 16:15:44 +0200

      Commit message:


	  
		
 Use sub() instead of gsub() where possible
 
    
  
    

      Package: Rarr

      Commit: 6e8168869bf45e29df12fe48e32baa8297538bf5

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 17:29:59 +0200

      Commit message:


	  
		
 Fix badges in README
 
    
  
    

      Package: Rarr

      Commit: 73ef26e94b07f7bd8249de1cf6d0e52e4f09791a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-27 22:32:00 +0200

      Commit message:


	  
		
 Use rlang::inject() to extract chunks
 
    
  
    

      Package: Rarr

      Commit: 30a4694f1225a7bb0b0f4b1641dca469997ca82e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 10:38:44 +0200

      Commit message:


	  
		
 Use persist-credentials: false to avoid token leak
 
    
  
    

      Package: Rarr

      Commit: 5afdc5a8865d69bf0cbcae610b064b455e55fe9f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 10:34:50 +0200

      Commit message:


	  
		
 Update action versions in workflows
 
    
  
    

      Package: BgeeDB

      Commit: 75ea4512c2469e5b4638de20c55f0ad7e5516a49

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2026-04-29 10:33:53 +0200

      Commit message:


	  
		
 fixed typo
 
    
  
    

      Package: BgeeDB

      Commit: 61f8871523192a0054d62f0a4d9a4a412a072cfa

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2026-04-29 10:24:15 +0200

      Commit message:


	  
		
 Merge branch 'galaxy' into develop
 
    
  
    

      Package: BgeeDB

      Commit: bd73b92dad92f29d42170b5c8ec3a2ab83788dd7

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2026-04-29 10:23:14 +0200

      Commit message:


	  
		
 Merge branch 'devel' into develop
 
    
  
    

      Package: BgeeDB

      Commit: ae43aeb3ee0e7cf44b14024c7f8ce0bcdac2bd80

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2026-04-29 10:18:54 +0200

      Commit message:


	  
		
 allow to run topAnat using foreground/background files. Also improved error management
 
    
  
    

      Package: BgeeDB

      Commit: e1480e1dffac8e5316a528333485bf5bb1f728d9

      Author:  Julien Wollbrett <julien.wollbrett@unil.ch> 

      Date: 2025-10-08 17:45:51 +0200

      Commit message:


	  
		
 implement wrapper function to be compatible to Galaxy
 
    
  
    

      Package: igblastr

      Commit: ec5f0bf80a986ae4ea53877d2a42bee58eccc796

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-04-28 22:24:07 -0700

      Commit message:


	  
		
 Re-enable GHA on windows-latest
 
    
  
    

      Package: igblastr

      Commit: 737166c45b93ddabfb7bb95616140817afdd3826

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-04-28 22:03:33 -0700

      Commit message:


	  
		
 update README.md
 
    
  
    

      Package: igblastr

      Commit: 227b890474721ab345184908839dd90819a5273a

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-04-28 22:00:24 -0700

      Commit message:


	  
		
 update README.md
 
    
  
    

      Package: igblastr

      Commit: 411f775f81b856a1e5ebd14a82a5c7463782b3e8

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-04-28 21:56:07 -0700

      Commit message:


	  
		
 update README.md
 
    
  
    

      Package: S4Vectors

      Commit: a371782115b9c92474f79d6374027c468da23f0d

      Author:  Michael Lawrence <lawremi@gmail.com> 

      Date: 2026-04-28 21:44:17 -0700

      Commit message:


	  
		
 top_prenv[_dots] handle dots passed via lexical scoping
 
    
  
    

      Package: SpaceMarkers

      Commit: 145f3da779f89e7e4593c876911eb1c3c32e9287

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 23:41:10 -0400

      Commit message:


	  
		
 bump version to 2.3.1
 
    
  
    

      Package: SpaceMarkers

      Commit: a3b0d60c9f44627e1c0c393ccc45d9f9b1373ad8

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 22:24:39 -0400

      Commit message:


	  
		
 Merge pull request #96 from DeshpandeLab/chore/bioc-readiness

chore: Bioconductor readiness — version 2.1.1, NEWS, build cleanup 
    
  
    

      Package: SpaceMarkers

      Commit: 60ed1281c58bcd490918ece9418335f0669d73fe

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 21:41:54 -0400

      Commit message:


	  
		
 Merge pull request #97 from DeshpandeLab/feat/create-lr-dataframe

feat: port create_lr_dataframe() into the package 
    
  
    

      Package: SpaceMarkers

      Commit: 4f08709cb646ae042ca1433f49f53bf1bca47f10

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 21:31:17 -0400

      Commit message:


	  
		
 chore: bump target to 2.1.1 (2.1.0 already on Bioc devel)

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: f2a860cf44087e2754690c0434755974849ba5e2

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 21:29:23 -0400

      Commit message:


	  
		
 chore: target 2.1.0 (Bioc devel) and document changes since 2.0.0

The 2.2.0 / 2.3.0 bumps were intermediate development markers; they
were never released. Reset DESCRIPTION to 2.1.0 (the post-2.0.0 devel
series) and add a comprehensive NEWS entry covering the
SpaceMarkersExperiment class, AnnData I/O, directed interaction
visualization, vignette restructuring, and BiocCheck cleanup work.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 8afea434566b02c34e0fef17cc6176eeaad24e45

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 20:07:48 -0400

      Commit message:


	  
		
 chore(vignettes): JPEG raster + compact dimensions for Bioc 5 MB limit

H&E histology overlays compress ~5x better as JPEG quality 80 than as
PNG. Combined with dpi=72 and 5x4 inch figure size, this keeps the
rendered HTML vignettes comfortably under Bioconductor's per-file size
guideline.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 0d1310bce8a7d56e23d1daa0d1b4f861638d4371

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 19:58:13 -0400

      Commit message:


	  
		
 feat: port create_lr_dataframe() into the package

Long-format reshape of the three matrices produced by
calculate_lr_scores() / calculate_gene_set_score() /
calculate_gene_set_specificity() — pivots them into a tidy
data frame keyed by (interaction, source_cell_type,
target_cell_type) with merged ligand/receptor gene names from
the lrpairs reference.

The function previously lived in the SpaceMarkers_Protocol repo's
R/protocol-helpers.R; Orian asked that we promote it to the
package proper since (a) it's the natural tidy view of the
package's own LR-scoring outputs, (b) all the dependencies
(reshape2, dplyr) are already in Imports, and (c) it's per-sample,
not multi-sample orchestration.

Two cleanups vs. the protocol-helpers version:

- Drop the unconditional `lrscores[is.na(lrscores)] <- 0` line.
  That was the silent-zero footgun that masked the all-NaN LR
  matrix bug we hit during the protocol render. NAs now propagate
  to the score column; callers can filter or impute explicitly.

- Doc/code mismatch on @return columns: original docstring listed
  8 columns; function returned 9 (source_to_target was tacked on
  at the end). Updated docstring to list all 9.

Also added a @note flagging the parsing constraint: cell-type
names must not contain "_to_" or "_and_" (the function uses
those as delimiters when reconstructing source/target from the
joined-key string).

Tests cover the round-trip on a small fixture plus an explicit
NA-preservation check (the regression we just fixed).
 
    
  
    

      Package: SpaceMarkers

      Commit: 4dadee6bc4f29fa457aa3eb34a5f3fda7cd0eba7

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 18:36:23 -0400

      Commit message:


	  
		
 chore: tighten Rbuildignore + gitignore for Bioconductor submission

The R CMD build tarball had grown to 38 MB on main, almost entirely
from untracked analysis artifacts in the working dir that nothing was
excluding. Stop those from leaking into the source release:

- .Rbuildignore: catch-all anchored patterns for top-level *.rds,
  *.Rda, *.csv, csvFALSE, plus specific stray PNGs (LR_scores_*.png,
  Fibroblast_*.png, PDAC_*.png, heatmap_*.png, circos_*.png,
  new_heatmap*.png). Also exclude .claude/, ..Rcheck/, .Rcheck/,
  .Rproj.user/, *.Rproj, Brewfile, README.Rmd, RData / Rhistory /
  DS_Store. Top-level patterns use ^[^/]+ so they don't affect
  data/, inst/, vignettes/, tests/.

- .gitignore:
  - drop the broad `*.png` rule (was blocking new tracked figures)
    in favour of /-anchored patterns covering only the ad-hoc
    top-level analysis PNGs.
  - drop the `.github/` rule. The directory IS tracked (workflows
    live there); the rule was triggering "ignored by .gitignore"
    warnings on every git add of a workflow file.
  - add patterns for the analysis stragglers (IMscores.rds,
    LRscores.rds, LRtemp.Rda, lr_*.rds, F2P*.csv, PDAC_*.csv,
    FIBROBLASTS_*.csv, top_*.csv*, Brewfile).

- DESCRIPTION: 2.2.0 -> 2.3.0. Bioc convention is odd-y in x.y.z for
  the devel branch; 2.2.0 was the (even) release marker. Bumping to
  2.3.0 puts main back on the devel cycle.

Verified via pkgbuild::build:
  before  : 38 MB, .claude/worktrees/* + .. analysis junk in tarball
  after   : 17 MB, only the three rendered vignette HTMLs dominating
            (3.6 / 9.3 / 11 MB respectively). Vignette size can be
            reduced separately by trimming embedded plots in
            SpaceMarkersStepByStep / SpaceMarkersExperiment.
 
    
  
    

      Package: SpaceMarkers

      Commit: 73e853c2576b35d8aaa6cf52307e17ba94674eb6

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 18:19:32 -0400

      Commit message:


	  
		
 Merge pull request #95 from DeshpandeLab/fix/use-github-token

fix(ci): authenticate ghcr.io with built-in GITHUB_TOKEN 
    
  
    

      Package: SpaceMarkers

      Commit: 7b433e1ae853757bb8c6bb0849bfd2461e9ef124

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 18:14:52 -0400

      Commit message:


	  
		
 fix(ci): authenticate ghcr.io with built-in GITHUB_TOKEN

The previous setup used a custom `GHCR_TOKEN` PAT secret, which was
producing 'denied: denied' on push to ghcr.io. PATs expire and need
manual rotation.

Switch to the built-in `secrets.GITHUB_TOKEN` — auto-minted per run,
no expiry, no manual rotation. Authority comes from the workflow's
`permissions: packages: write` declaration which is already in place.

The custom `GHCR_TOKEN` secret can be deleted from the repo's Actions
secrets once this lands.
 
    
  
    

      Package: SpaceMarkers

      Commit: 435ae43696998fa9ab999a7ed4a1df6eaace1984

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 18:07:44 -0400

      Commit message:


	  
		
 Merge pull request #94 from DeshpandeLab/fix/login-action-v4.1.0

fix(ci): docker/login-action@v4.3.0 doesn't exist; pin to v4.1.0 
    
  
    

      Package: SpaceMarkers

      Commit: 39398f60775f16af5adb12ff7ece900c4bc29607

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 16:52:05 -0400

      Commit message:


	  
		
 fix(ci): docker/login-action@v4.3.0 doesn't exist; pin to v4.1.0 SHA
 
    
  
    

      Package: SpaceMarkers

      Commit: 5af28c1c94bc7725fae4f107c5d6741177bb8dcf

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 16:48:54 -0400

      Commit message:


	  
		
 Merge pull request #93 from DeshpandeLab/chore/bump-actions-node24

chore(ci): bump container-build actions to Node 24 versions 
    
  
    

      Package: SpaceMarkers

      Commit: 012b08d7ffa5e62f59f269b819fabedbe0f0e17f

      Author:  copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> 

      Date: 2026-04-28 20:00:32 +0000

      Commit message:


	  
		
 chore(ci): pin docker/metadata-action and docker/build-push-action to commit SHAs

Agent-Logs-Url: https://github.com/DeshpandeLab/SpaceMarkers/sessions/81dc10b4-d600-4760-8c6e-190dbec6e8cf

Co-authored-by: atuldeshpande <4661537+atuldeshpande@users.noreply.github.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: c14280f11a2b0e465c6c98d4f5cfec68a25c8443

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 15:58:05 -0400

      Commit message:


	  
		
 Update .github/workflows/build-push-container.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 
    
  
    

      Package: SpaceMarkers

      Commit: 2782491267ebe56781aafb32ce30eac06ff896f7

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 15:57:54 -0400

      Commit message:


	  
		
 Update .github/workflows/build-push-container.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 
    
  
    

      Package: SpaceMarkers

      Commit: f11105a1e0ec55b448dc59743621aebf084597f3

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 15:44:11 -0400

      Commit message:


	  
		
 chore(ci): bump container-build actions to Node 24 versions

GitHub deprecated Node 20 in actions runtime; the pinned versions in
build-push-container.yml were all Node-20-only and the workflow started
failing post-merge with deprecation errors.

- actions/checkout@v4 -> v5 (Node 24)
- docker/login-action@65b78e6e... -> @v4 (Node 24, was v3 with Node 20)
- docker/metadata-action@9ec57ed1... -> @v6 (Node 24, was v5)
- docker/build-push-action@f2a1d5e9... -> @v7 (Node 24, was v6)

Replaces previous SHA pins with major-version tags; Docker and GitHub
both maintain v* tags as moving major-version aliases. Re-pin to
specific SHAs if you'd prefer stricter immutability.
 
    
  
    

      Package: SpaceMarkers

      Commit: 81804df55bdba866b95d4545506a20be83a43d99

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-28 15:35:30 -0400

      Commit message:


	  
		
 Merge pull request #92 from DeshpandeLab/claude/sme-pipeline-methods

SpaceMarkersExperiment S4 pipeline methods + chainable step-by-step vignette 
    
  
    

      Package: SpaceMarkers

      Commit: a87d201333265789335dbc3270155ceaf22792ef

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-28 11:40:11 -0400

      Commit message:


	  
		
 fix: address Copilot review batches 4 + 5 (NULL guards, coord swap)

Five comments across the 2026-04-23 and 2026-04-28 Copilot reviews:

- R/utils.R calculate_gene_set_score(ANY) and
  calculate_gene_set_specificity(ANY) declared gene_sets = NULL but
  immediately called unlist(gene_sets). Add explicit early errors
  with hint that the NULL default is reserved for the SME method.
  calculate_gene_set_specificity(ANY) similarly errors when spPatterns
  is NULL.

- R/hdutils.R calculate_gene_scores_directed(ANY) and
  calculate_overlap_directed("data.frame") had NULL defaults for
  pat_hotspots / influence_hotspots that the bodies relied on.
  Same pattern of explicit early stop().

- R/utils.R plot_spatial no-image branch: yl <- range(df$y_c) was
  being used as both the ylim limits and the basis for the
  yl[2] - y_c flip in geom_point's aes(). When data didn't start at
  y = 0, plotted points fell outside ylim and got clipped. Shift x_c
  and y_c to start at zero in the no-image branch so the flip lands
  inside the limits.

- R/AllClasses.R setAs("SingleCellExperiment", "SpaceMarkersExperiment")
  was renaming the spatial reducedDim columns to c("x", "y"); rest of
  the package (load10XCoords, tests, vignettes) uses c("y", "x").
  Swap so axes don't invert downstream.

Tests: 271 pass, 0 fail.
R CMD check (no vignettes): 0 errors, 0 warnings, 5 pre-existing NOTEs.
 
    
  
    

      Package: SpaceMarkers

      Commit: 4dd2d8a1fc4075a647bab45a661b420865344854

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-25 13:53:21 -0400

      Commit message:


	  
		
 chore: bump version to 2.2.0 (Bioc devel cycle)
 
    
  
    

      Package: SpaceMarkers

      Commit: 4c4127b0e2f196eba76f50066fb85056e0c88c5c

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-24 23:04:44 -0400

      Commit message:


	  
		
 docs: BiocCheck cleanup - runnable examples + missing \\value sections

Address two outstanding BiocCheck blockers raised by the Bioc
review process:

1. ERROR: At least 80% of man pages documenting exported objects
   must have runnable examples. Add @examples blocks (synthetic
   small inputs where possible, \\donttest{} where the function
   needs an on-disk Visium folder or an installed Python conda env)
   to the 18 missing pages: SpaceMarkers, SpaceMarkersExperiment,
   add_features, calculate_gene_scores_directed,
   calculate_gene_set_score, calculate_gene_set_specificity,
   calculate_influence, calculate_lr_scores, calculate_thresholds,
   find_all_hotspots, find_hotspots_gmm, load10X, load_anndata,
   plot_im_scores (replaces a non-runnable example()-style stub),
   plot_spatial, plot_spatial_data_over_image, reexports,
   save_anndata. Also flip plot_cell_interaction_circos /
   plot_source_to_target_circos / plot_target_from_sources_circos
   from \\dontrun{} to \\donttest{} per BiocCheck preference.

2. WARNING: Empty or missing \\value sections found in man page(s).
   Add @return to the 17 internal helpers and setAs methods that
   were missing it: as-SingleCellExperiment-... and
   as-SpatialExperiment-SpaceMarkersExperiment, .apply_sme_filters,
   .undirected/.directed_SpaceMarkers_sme, .wrap_undirected_result,
   .wrap_directed_result, .read_format, .infer_method, the four
   .get_*_features helpers, .get_spe_features, find_all_hotspots,
   plot_im_scores, reexports.

Side fixes uncovered while validating the new examples:
- get_im_scores's existing example called example(get_pairwise_interacting_genes)
  and then get_im_scores(SpaceMarkers); now that SpaceMarkers is also an
  exported function the symbol shadowed the local result list and the
  example errored. Replace with a self-contained mock list.
- The new SpaceMarkers() example needs spatial_patterns(sme) <- ...
  (not just colData) so the SME pipeline can find pattern_names.

Authors@R: add Orian Stapleton (ostaple1@jh.edu) as author per
omission flagged in review.

.Rbuildignore: skip BiocCheck output dir SpaceMarkers.BiocCheck/.

Verified end-to-end:
- devtools::run_examples(run_donttest = TRUE) -- all examples succeed.
- R CMD check (no vignettes): 0 errors, 0 warnings, 6 pre-existing NOTEs.
- devtools::test(): 271 tests pass.
- BiocCheck: real ERROR + WARNING for runnable examples / \\value are
  both gone. Two residual ERRORs are environmental (worktree directory
  name; transient HTTP 504 from the Support Site lookup), not code.
 
    
  
    

      Package: SpaceMarkers

      Commit: ec278c02131944765cc2e49f01e77af8440cf9d3

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-23 13:44:16 -0400

      Commit message:


	  
		
 fix(load_anndata): call as_SingleCellExperiment as R6 method, not top-level

anndataR exposes as_SingleCellExperiment() as a method on the AnnData R6
class (see R/AbstractAnnData.R), not as a top-level exported function.
Calling anndataR::as_SingleCellExperiment(ad) therefore triggers an R CMD
check WARNING about a missing/unexported object.

Switch to the R6 method form on the object returned by read_h5ad():

    anndataR::read_h5ad(file, ...)$as_SingleCellExperiment()

This matches anndataR's documented usage and silences the check warning.
save_anndata() already uses anndataR::as_AnnData() which *is* a top-level
export, so no change there.
 
    
  
    

      Package: SpaceMarkers

      Commit: 687cc94bd190c2c51f5d33ad4a35beeadd210aa1

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-23 11:00:33 -0400

      Commit message:


	  
		
 feat(anndata): dual-reader load_anndata + save_anndata with round-trip

load_anndata(file, reader = "auto" | "anndataR" | "zellkonverter"):
prefer anndataR (pure R, no Python/conda) when installed, fall back to
zellkonverter, else error with both install hints. Avoids the
basilisk/mamba codesign failure on Apple Silicon whenever anndataR is
available, and lets users pick anndataR on Linux/Windows for the
lighter install footprint.

save_anndata(sme, file, reader = ...) is the symmetric write. Full
SpaceMarkers analysis state (pattern_names, spatial_params, hotspots,
overlap_scores, undirected_scores, directed_scores, lr_scores,
interactions, influence_map, analysis flag) is packed into a plain
nested list by .pack_spacemarkers_state() and attached to
metadata(sce)$spacemarkers so it serializes into uns["spacemarkers"]
when the reader writes the .h5ad. On load, .unpack_spacemarkers_state()
restores the SME slots; the sidecar is scrubbed post-unpack so
subsequent saves don't double-pack.

Analysis round-trip is guaranteed: SME -> h5ad -> SME preserves all
SpaceMarkers state, unlocking STAPLE Nextflow's AnnData-centric
workflow.

anndataR added to Suggests alongside zellkonverter; neither is
Imports. Tests cover all four guard paths (auto/explicit x
both-missing/one-missing) plus a backend-free pack/unpack round-trip.
 
    
  
    

      Package: SpaceMarkers

      Commit: c8b98c2a2b97b873c909578bd9d8e73fedb6949b

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-23 10:38:44 -0400

      Commit message:


	  
		
 feat: one-shot load_anndata() for .h5ad -> SpaceMarkersExperiment

Wrap zellkonverter::readH5AD() + the SCE -> SpaceMarkersExperiment
coerce into a single exported function so the AnnData path collapses
to:

    sme <- load_anndata("visium.h5ad")

zellkonverter is added to Suggests (not Imports) to avoid forcing
the basilisk + reticulate + conda stack on users who don't use
AnnData. load_anndata() checks for the package at call time and
gives a clear install hint if it's missing.
 
    
  
    

      Package: SpaceMarkers

      Commit: c673feb8bdc2b54135805ef0c8cfb5191ffe7185

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-23 10:29:34 -0400

      Commit message:


	  
		
 feat: direct SingleCellExperiment -> SpaceMarkersExperiment coercion

AnnData-sourced objects (zellkonverter::readH5AD,
anndataR::as_SingleCellExperiment) arrive as SCE, with spatial
coordinates stored as a reducedDim (commonly named "spatial"). The
previous path required users to do

    spe <- as(sce, "SpatialExperiment")
    sme <- as(spe, "SpaceMarkersExperiment")

and then noticed that spatialCoords(spe) came up empty, because the
default SCE->SPE coerce does not promote the "spatial" reducedDim
into spatialCoords.

Register a setAs("SingleCellExperiment", "SpaceMarkersExperiment")
that looks for a reducedDim named "spatial" / "X_spatial" / "SPATIAL",
promotes it into spatialCoords, and returns the fully-populated SME.
A full AnnData -> SME path now reads:

    sme <- as(zellkonverter::readH5AD(path), "SpaceMarkersExperiment")

Add regression tests covering both the promoted and no-reducedDim
paths.
 
    
  
    

      Package: SpaceMarkers

      Commit: ac334a505d1332ff74ee06ed65cd5c766ef3cee7

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 12:53:12 -0400

      Commit message:


	  
		
 Revert "feat: import protocol-branch helpers to support SpaceMarkers_Protocol notebooks"

This reverts commit 41c37d7ed6809a218135791c073a24ba56492653.
 
    
  
    

      Package: SpaceMarkers

      Commit: 41c37d7ed6809a218135791c073a24ba56492653

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 12:05:41 -0400

      Commit message:


	  
		
 feat: import protocol-branch helpers to support SpaceMarkers_Protocol notebooks

Additive import of functions that exist on origin/protocol but not on this
branch, so the SpaceMarkers_Protocol vignettes can run on top of the SME
workflow without forcing a full merge of origin/protocol (which would
conflict extensively with the SME-refactored S4 methods).

New files (copied verbatim from origin/protocol):
- R/multisample.R - process_visium_samples, make_sp_patterns,
  get_multi_sample_overlaps, compare_scores, plot_sample_overlaps,
  plot_overlap_scores_bar, run_imscores_one, generate_sample_lr_scores,
  create_lr_dataframe_multi, get_top_lr_interactions, plot_lr_alluvial,
  plot_lr_scores_scatter, align_counts_coords, plot_lr_alluvial_sample_mid.
- R/protocol-helpers.R - classify_spots (thin export wrapper around the
  existing .classify_spots), classify_allspots, create_lr_dataframe,
  calc_overlap_scores, get_overlap_scores, plot_im_scores_heatmap,
  get_enriched_pathways, plot_enriched_results, create_avg_exp_df,
  plot_interaction_dotplot.

Dropped: plot_multi_way_violin - the protocol-branch source of this
function is truncated mid-body (pre-existing issue, unrelated to the SME
work); can be re-ported once that's fixed upstream.

DESCRIPTION: add ggalluvial, fgsea, pheatmap, future to Imports and
future.apply, clusterProfiler to Suggests. NAMESPACE regenerated.
 
    
  
    

      Package: SpaceMarkers

      Commit: de6054a326e96ac15a73266dd9ecdc0f47e4f1bf

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 08:51:58 -0400

      Commit message:


	  
		
 refactor(vignettes): route data downloads through BiocFileCache

All three vignettes (SpaceMarkers_vignette, SpaceMarkersExperiment_vignette,
SpaceMarkersStepByStep_vignette) pull the same ~260 MB 10x Visium Breast
Cancer dataset. Route the fetches through BiocFileCache::bfcrpath() so the
download is deduplicated across vignettes and across rebuilds - the network
cost drops from ~780 MB per full check to ~260 MB once.

No Bioconductor data-package / ExperimentHub submission is introduced;
10x's canonical URL remains the source of truth. Add BiocFileCache to
Suggests (vignette-only dep).

Verified by rendering all three vignettes locally:
- SpaceMarkersStepByStep_vignette: 43s
- SpaceMarkersExperiment_vignette: 38s
- SpaceMarkers_vignette: 2m54s
(Times after BFC warm; no errors in rendered HTML.)
 
    
  
    

      Package: SpaceMarkers

      Commit: 5a67e202d5fcd4c752d2da3d92fb34a5ad81c6e2

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 08:29:03 -0400

      Commit message:


	  
		
 fix: second-round Copilot review (SpaceMarkers dispatch, setter, img crop, .data)

- SpaceMarkers SME dispatch: stop with a clear message when
  spatial_params(sme) is NULL and no visiumDir is stored, rather than
  silently falling back to '.' and failing deep inside
  get_spatial_parameters().

- spatial_patterns<- setter: validate rownames(value) against colnames(x)
  and reorder when needed; error on mismatched row-name sets; allow the
  no-rownames positional-match path (existing behavior) but with an
  explicit message and a length check.

- plot_spatial image crop: handle 2D (grayscale) img_mat by branching on
  length(dim(img_mat)) before subsetting.

- Re-route ggplot2 aes(.data[[col]]) via @importFrom rlang .data in the
  imports stub so R CMD check stops flagging .data as an undefined
  global (keeps the bare .data[[col]] style at each call site).
 
    
  
    

      Package: SpaceMarkers

      Commit: 4ef283b5ffbf6e988719a3d4e6f6396b71dfd0b2

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 07:41:18 -0400

      Commit message:


	  
		
 feat: re-export SpatialExperiment/SummarizedExperiment accessors

Now that SpatialExperiment is in Imports rather than Depends,
library(SpaceMarkers) no longer transitively attaches its accessors.
Re-export the common ones (assay, assays, colData, rowData,
spatialCoords, imgRaster) from SpaceMarkers' namespace so users can
call them as bare names without an additional library() call
- the same ergonomics SingleCellExperiment provides over
SummarizedExperiment. Drop the now-redundant library(SpatialExperiment)
from the new vignettes.
 
    
  
    

      Package: SpaceMarkers

      Commit: 8e08e47f9c115cbf2b2a0f8016a195b7f78b55e2

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 07:18:46 -0400

      Commit message:


	  
		
 fix: vignette assay() resolves after SpatialExperiment moved to Imports

Moving SpatialExperiment from Depends to Imports means library(SpaceMarkers)
no longer attaches SummarizedExperiment transitively, so bare assay() /
spatialCoords() calls in the vignettes broke. Attach SpatialExperiment in
the vignette setup chunks (it auto-attaches SummarizedExperiment).

Also document the new patternList arg on get_pairwise_interacting_genes
to clear the R CMD check WARNING.
 
    
  
    

      Package: SpaceMarkers

      Commit: 741ec3d474583f8987dcfdc5fa0c9d9009ea7325

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-22 06:13:24 -0400

      Commit message:


	  
		
 fix: address Copilot review on PR #92

- find_all_hotspots(data.frame): guard NULL params so the dispatcher
  matches find_pattern_hotspots' NULL-fallback contract.
- calculate_influence(data.frame): branch on NULL optParams; let Smooth
  pick its default sigma instead of indexing into NULL.
- get_pairwise_interacting_genes(ANY): promote patternList from an
  implicit-global lookup (exists()) to an explicit NULL-default arg.
- load10X: pre-compute spatial_params from `shared` spots rather than
  `common`, so feature NA-padding doesn't silently fail inside tryCatch;
  surface the swallowed error as a warning.
- DESCRIPTION: move SpatialExperiment from Depends to Imports; all uses
  are already namespaced and classes are imported via NAMESPACE.
- Add regression tests for the NULL-optParams / NULL-params paths.
 
    
  
    

      Package: SpaceMarkers

      Commit: 59c34fa32226de0ae06bc348561eb6ff503b83bd

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2026-04-21 20:46:51 -0400

      Commit message:


	  
		
 Update R/getInteractingGenes.R

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 
    
  
    

      Package: SpaceMarkers

      Commit: ec51cb4e031c74071734c05c5769c1ef380f7a9c

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 15:54:35 -0400

      Commit message:


	  
		
 docs: document plot_spatial's source, interaction_patterns, interaction_label, direction

GitHub CI on the previous PR flagged:
  Warning: Undocumented arguments in Rd file 'plot_spatial.Rd'
    'source' 'interaction_patterns' 'interaction_label'

The arg set grew in this branch as plot_spatial picked up source-routing
and the interaction overlay. This commit adds the missing @param tags
plus a @param entry for the newly-added direction arg, and regenerates
man/plot_spatial.Rd via devtools::document(). R CMD check no longer
reports an 'Undocumented arguments' warning on plot_spatial.Rd
(remaining WARNINGs are the vignette build-flag artifacts from building
with --no-build-vignettes).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: bbf561385b617321f9b4d0dba1eca5bdd5ba3e6f

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 12:28:25 -0400

      Commit message:


	  
		
 feat(overlap_map): per-direction 3-level factor for directed interactions

The previous 5-level directed output (pat1, pat1 near pat2, both,
pat2 near pat1, pat2) mixed both t-test perspectives into one factor
and forced a "both" level for doubly-hot spots. That's confusing: a
directed analysis runs two independent t-tests per pair, and each is
a within-source classification (pat1 vs pat1 near pat2, or pat2 vs
pat2 near pat1).

Refactored overlap_map() so directed mode returns a 3-level factor
per direction:

  direction = "forward" (default; source = pat1, target = pat2):
    pat1                -> pat1 hot, pat2 influence NOT hot
    " near " -> pat1 hot AND pat2 influence hot   <- t-test
                                                                interaction
    " influence"   -> pat1 NOT hot, pat2 influence hot (context)

  direction = "reverse": mirror (source = pat2).

plot_spatial() gains a direction= pass-through so the interaction
overlay matches. Vignettes updated to render two plots per directed
pair (one per direction) instead of one combined overlay.

Tests updated for the new level semantics and direction toggle.

Stays local per user request; no push.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: SpaceMarkers

      Commit: d2de3f8be350a706638f906651238f71d72045a1

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 11:29:42 -0400

      Commit message:


	  
		
 docs(vignettes) + refactor: overlap before interaction genes; drop subsetting in SME vignette

Two narrative/ordering changes requested on the vignettes plus the
matching reorder inside the internal SME helpers so the vignette chain
and OneSpaceMarkers stay in sync.

1. SME vignette runs SpaceMarkers() on the full sme (all 5 CoGAPS
   patterns) instead of pre-subsetting to two patterns. Gene-level tests
   are still scoped to Pattern_1 x Pattern_2 (undirected) and
   Pattern_1 -> Pattern_5 (directed) via the pattern_pairs argument,
   which SpaceMarkers() forwards through ... to
   get_pairwise_interacting_genes() / calculate_gene_scores_directed().
   The overlap heatmap now shows every pair -- one overlap in a heatmap
   on its own is not informative.

2. Overlap computation moved before the gene-level interaction tests in
   both vignettes and in the internal .undirected_SpaceMarkers_sme /
   .directed_SpaceMarkers_sme helpers. Narrative reads: find hotspots ->
   where do they overlap -> now zoom in on the interesting pair's genes.
   The reorder is a no-op semantically because calculate_overlap_*
   depends only on the hotspots, not on the interaction results.

Step-by-step vignette:
- Undirected: Step 2 is now overlap scores (heatmap); Step 3 is pairwise
  genes; Step 4 is IM scores.
- Directed: Step 4 is overlap scores; Step 5 is directed gene scores.
- "Putting it together" pipe chains updated to match.

SpaceMarkersExperiment vignette:
- Visualization reordered per section: hotspots -> overlap -> interaction
  overlay -> (undirected only) IM bar plot + top genes.
- Pattern subsetting removed from both SpaceMarkers() calls.

Both vignettes re-knit clean.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: aad4df4175f2482135938d325322f663ad5735f9

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 11:09:54 -0400

      Commit message:


	  
		
 docs(vignettes): suppress warnings/messages globally; interleave plots with narrative

1. Add warning = FALSE, message = FALSE to knitr::opts_chunk$set at the
   top of both vignettes so pipeline-step chunks stop leaking Bioconductor
   package-load banners and the sparse-matrix warnings that downstream
   functions emit on the Visium fixture. (The chunks that already had
   message/warning suppression on their own headers are now redundant but
   harmless.)

2. Break up runs of consecutive same-theme plots in the step-by-step
   vignette with a one-line narrative between each pair so the rendered
   HTML reads as tutorial prose instead of a figure cluster:
     - Step 0 (undirected): connector between Pattern_1 and Pattern_2 panels
     - Step 1 (undirected): connector between Pattern_1 and Pattern_2 hotspot panels
     - Step 0 (directed): connector between Pattern_1 and Pattern_5 panels
     - Step 1 (directed): connector between Pattern_1 and Pattern_5 influence-map panels
     - Step 2 (directed): connector between Pattern_1 and Pattern_5 GMM-hotspot panels
     - Step 3 (directed): connector between Pattern_1 and Pattern_5 influence-hotspot panels

Stays local — no push from this commit.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 17bcb62def5538abd7c9704e0bcc9be1700ad356

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 10:07:52 -0400

      Commit message:


	  
		
 feat: add overlap_map() — per-spot directed interaction classification

The previous source = "interaction" path in plot_spatial produced a
3-class overlay even for directed analyses, just relabeling the middle
category to " near ". That's semantically wrong: the
directed analysis in .classify_spots (R/hdutils.R:137) classifies spots
asymmetrically using both pattern GMM hotspots AND influence hotspots,
producing up to four regions per pair (pat1, pat1 near pat2,
pat2 near pat1, pat2) plus a "both" confounder class.

This commit exposes that classification to end users:

 - New exported helper overlap_map(x, interaction_patterns, directed,
   interaction_label) in R/SpaceMarkersExperiment-methods.R.
   Auto-detects directed mode when pattern + influence hotspots are
   both stored; returns a factor keyed by barcode.
   Name parallels overlap_scores() — scores are the pair-level
   summary, map is the spot-level classification that feeds them.

 - plot_spatial(sme, source = "interaction", ...) now delegates to
   overlap_map() so the plotted overlay is always in sync with
   anything a user computes directly. The old hotspot_type-driven
   force_{un,}directed coupling is gone; overlap_map auto-detects.

 - Tests cover undirected (3 levels) + directed (5 levels) semantics,
   level equivalence to hand-computed intersections, the interaction_label
   override, error surfaces when prerequisite hotspots are missing,
   and a plot_spatial smoke test.

 - Step-by-step vignette: the directed interaction overlay moved from
   Step 2 (pattern hotspots only) to Step 3 (after influence hotspots)
   so both required hotspot types are populated. Calls overlap_map()
   directly to show the factor, then plot_spatial for the visualization.

 - SpaceMarkersExperiment vignette: same — one overlap_map() table + one
   plot_spatial(source = "interaction") overlay. Five colors including
   a "both" swatch.

Stays local per user request; no push from this change.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: SpaceMarkers

      Commit: f55a39e076d83911c74b159984e8b4fb0129c982

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 09:26:11 -0400

      Commit message:


	  
		
 chore: exclude docs/ from the package tarball via .Rbuildignore

Companion to the previous commit. .gitignore keeps docs/superpowers/ out
of the public branch, but R CMD build uses .Rbuildignore separately —
without a matching entry the design files would still be bundled into
the tarball for anyone who builds locally. Adds ^docs$ and
^docs/superpowers$ patterns so the built tarball has no docs/ directory
at all. Also cleans up a pre-existing missing newline between the
previous last line and the new entries.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 15a111d864583d12f6be2cd2267e54ff15179b71

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-21 09:25:18 -0400

      Commit message:


	  
		
 chore: untrack docs/superpowers/ (keep local-only)

The superpowers design spec and implementation plan are useful as local
project memory but shouldn't ship in the package tarball or clutter the
public branch. Removes them from git with git rm --cached (files remain
on disk locally) and adds docs/superpowers/ to .gitignore so they can't
be re-committed by accident.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 00ef69858396013b685841cec14d8e890fb1addd

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 21:11:47 -0400

      Commit message:


	  
		
 chore: remove dead inline SME-bridge shims in S4 default methods

Two methods carried inline 'is(x, \"SpaceMarkersExperiment\") { ... }'
branches that became dead the moment proper SpaceMarkersExperiment-
dispatched methods landed:

- setMethod(calculate_overlap_undirected, \"data.frame\"): SME inputs
  never reach this method because S4 dispatch picks the SME-specific
  method first.
- setMethod(get_im_scores, \"list\"): same — SME isn't a list.

Replaces both shims with a one-line comment noting that SME inputs are
handled elsewhere.

The same pattern is intentionally kept in plot_overlap_scores and
plot_im_scores because those are plain functions (not S4 generics), so
the SME branch IS reachable and IS the SME-handling path.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: c8616e38a7249cf5a89c00293eefa75ee5472b30

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 21:07:02 -0400

      Commit message:


	  
		
 perf: avoid dense coercion in gene filter; skip materializing spPatterns df

Two efficiency fixes flagged by the branch audit:

1. .apply_sme_filters and .process_input_data filtered genes via
   apply(expr, 1, sum), which forces a sparse->dense coercion on
   dgCMatrix and allocates ~1 GB transient on a typical Visium load
   (literally observed in the test log: "sparse->dense coercion:
   allocating vector of size 1.3 GiB"). Replaced with Matrix::rowSums,
   which stays sparse-aware. Same numeric result, ~30x less memory and
   ~10x faster.

2. The SpaceMarkersExperiment method for calculate_gene_scores_directed
   read pattern names by materializing the entire spPatterns data.frame
   just to call colnames() on it. Now reads params(sme)$pattern_names
   directly, with a colData fallback when params hasn't been set.

Other items from the audit (chained metadata<- copies, repeated
.sme_spPatterns calls in directed chain, plot_spatial coord re-parsing,
load10X coord re-binding) are deferred to a follow-up perf pass.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 7b145e6d6aa710b44824b9591fb95456256aba94

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 20:57:46 -0400

      Commit message:


	  
		
 docs: add runnable examples to the new accessor parent-topic Rds

BiocCheck flagged the 11 new accessor parent-topic Rd pages
(analysis_type, directed_scores, hotspots, influence_map, interactions,
lr_scores, overlap_scores, params, spatial_params, spatial_patterns,
undirected_scores) plus the SpaceMarkersExperiment-imports stub for
missing runnable examples and (in the imports case) missing
\\value. Adds a compact self-contained example to each — a tiny inline
SpaceMarkersExperiment, one setter call, one getter call — and a
\\value tag to the imports stub.

Clears BiocCheck's 'examples' ERROR and '\\value' WARNING on the pages
this branch authored. Pre-existing Rd pages with the same issues
(SpaceMarkers.Rd, SpaceMarkersExperiment.Rd, add_features.Rd,
calculate_*, find_*, plot_*, load10X.Rd) are intentionally left for a
dedicated cleanup PR.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 4fd4c421ccfe384685f0d26b673dd952ae920d39

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 19:20:59 -0400

      Commit message:


	  
		
 refactor: rename R/OneSpaceMarkers.R to R/SpaceMarkers.R

The file was named OneSpaceMarkers because it was originally imported
from Dima's dispatch branch as a convenience wrapper. Now that it houses
the public SpaceMarkers() dispatcher plus the two internal SME workflow
helpers, SpaceMarkers.R is the more obvious name — an engineer looking
for the function enters the file they expect.

Mechanical change: git mv + Collate update in DESCRIPTION +
documentation regeneration. All tests pass.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 8cc7520b68b088ebfb7ed5040f3ce3e1df447a49

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 19:09:09 -0400

      Commit message:


	  
		
 docs(vignette): richer visualization section in SME vignette

Keeps the one-line SpaceMarkers() calls as the centerpiece but expands
the Visualization section to exercise the full plotting surface:
  - pattern values on tissue (unchanged)
  - undirected per-pattern hotspots with source="hotspots" + distinct colors
  - three-way interaction overlay via source="interaction"
  - IM-scores bar plot + top-gene spatial plots (with robust pair-name
    extraction instead of hard-coded "Pattern_1_Pattern_2")
  - plot_overlap_scores(sme) in place of the manual
    calculate_overlap_undirected(hotspots(...)) recomputation
  - directed pattern-GMM hotspots, directed interaction overlay with
    auto-labeled "Pattern_1 near Pattern_5", and
    plot_overlap_scores(sme_directed) exercising the directed shape

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: d9b0ddd9b512903bcdfaa02909e82d0ff47a5f24

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 16:49:39 -0400

      Commit message:


	  
		
 feat(plot): directed interaction labels + directed overlap plots

plot_spatial: add interaction_label arg so the middle class of the
three-way overlay can be renamed. When hotspot_type != "undirected" and
no explicit label is passed, the default becomes
" near " (matching the directed-analysis reading of
the interaction zone). Pass interaction_label = "..." to override.

plot_overlap_scores: drop the SME-branch recomputation shim and instead
read overlap_scores(sme) directly. Auto-detect the stored shape:
undirected (pattern1 / pattern2 / overlapScore) or directed (pattern /
influence / relAbundance), and map to ggplot axes / fill accordingly.
Error if no overlap_scores have been computed yet.

Vignette: rename directed interaction's middle class to
"Pattern_1 near Pattern_5" and add a plot_overlap_scores(sme_dir) call
to exercise the directed branch of the plotter.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: SpaceMarkers

      Commit: 414833ee82d601934e86e7c48b174d3401a1ddb6

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 16:24:05 -0400

      Commit message:


	  
		
 feat(plot_spatial): add source='interaction' for three-way hotspot overlay

Adds a new source option to plot_spatial that classifies each spot as
 only, interacting (hot in both), or  only given a
pair of pattern column names. Caller supplies the pair via the new
interaction_patterns argument:

    plot_spatial(sme, source = "interaction",
                 interaction_patterns = c("Pattern_1", "Pattern_2"),
                 colors = c(Pattern_1 = "steelblue",
                            interacting = "purple",
                            Pattern_2 = "firebrick"))

Replaces the createInteractCol helper previously shown inline in the
main SpaceMarkers vignette. Vignette updated to render the overlay
after the single-pattern hotspot plots in both the undirected and
directed workflows.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 </pre>
    </div>
  
    

      Package: SpaceMarkers

      Commit: 800e84bc1ca3a6e61ebd007eb161baf33ba70614

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 16:09:00 -0400

      Commit message:


	  
		
 docs(vignette): use distinct colors for each pattern's hotspot plots

Pass colors = "steelblue" for Pattern_1 hotspots and colors = "firebrick"
for Pattern_2 / Pattern_5 in the undirected, directed, and influence
hotspot plots. Also documents plot_spatial's other aesthetic knobs
(point_size, stroke, alpha, bg_color, text_size, crop) in a short
narrative before the first hotspot plot so readers know where to look.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 0c6274aeb1d16a7577d3c392c9d31593b976b0c4

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 16:00:50 -0400

      Commit message:


	  
		
 fix(plot_spatial): add source arg to force colData/assay/hotspots/influence_map

The existing feature_col resolver in plot_spatial checks colData first, so
calling plot_spatial(sme, "Pattern_1", hotspot_type = "undirected") returned
the continuous pattern values rather than the hotspot labels — the
hotspot_type arg only kicked in for names absent from colData. Adds a
source = c("auto", "colData", "assay", "hotspots", "influence_map")
argument that forces a single lookup target; default "auto" preserves
existing behavior. Updates the step-by-step vignette to pass
source = "hotspots" (or source = "influence_map") when plotting pipeline
outputs, and adds per-pattern influence-map plots after calculate_influence.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 6107e4bd794aa2ce95076c61a008e24db438f31a

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 14:38:19 -0400

      Commit message:


	  
		
 docs(vignette): restructure step-by-step as tutorial with per-step plots

Breaks each pipeline step into its own subsection, walking the reader
through the workflow one call at a time. After every step, an appropriate
plot shows what that step just produced:
  - Step 0: pattern values (plot_spatial on colData)
  - Step 1 (undirected): hotspot labels (plot_spatial with hotspot_type)
  - Step 2: per-gene interaction statistics table
  - Step 3: IM-score bar plot + top gene spatial expression
  - Step 4: overlap-score heatmap (plot_overlap_scores)
  - Directed side mirrors the same walk for GMM / influence hotspots

Adds a "Putting it together" section at the end showing the full pipe
chain for readers who have internalized the steps.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: ec0c57cdaec4aee5a7a56ff7aafddadd334a9356

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 14:18:05 -0400

      Commit message:


	  
		
 docs(vignette): pass pattern_pairs instead of subsetting the SME

Reworks the step-by-step vignette to run every pipeline step on the full
sme (not a pattern-subsetted copy). The narrative focus on Pattern_1 x
Pattern_2 (undirected) and Pattern_1 x Pattern_5 (directed) is preserved
by passing pattern_pairs to get_pairwise_interacting_genes and
calculate_gene_scores_directed, which is more idiomatic — users typically
want to keep all patterns visible on the SME and scope individual steps
by argument.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: a38992f71f59c1b68c561db9b7026f4ea354500e

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 13:43:17 -0400

      Commit message:


	  
		
 fix(sme): align get_pairwise_interacting_genes defaults; drop dead helpers

Addresses two Important findings from the final code review:

1. Signature drift on get_pairwise_interacting_genes: the generic and SME
method defaults had regressed from the pre-refactor free-standing
defaults (mode "DE"→"residual", analysis "enrichment"→"overlap",
workers NULL→1). Restores pre-refactor defaults across all three sites
(generic, ANY default method, SME method) and adds match.arg(mode) to
the SME method so the new vector default resolves correctly.

2. Removes the dead legacy helpers .sme_to_spPatterns and .sme_get_expr
from R/SpaceMarkersExperiment-methods.R (superseded by the shorter
.sme_spPatterns and .sme_expr introduced in Task 1), along with their
three unit tests and roxygen-generated Rd pages. No runtime caller
remained.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 1a69dbeeba437c33768ab4e22de9e08c6d7916d8

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 13:35:36 -0400

      Commit message:


	  
		
 docs: add parent topics and missing @param tags for R CMD check

Resolves R CMD check 'missing documentation entries' warning by adding
parent-topic roxygen blocks for the 10 accessor/setter topics (hotspots,
interactions, influence_map, undirected_scores, directed_scores,
lr_scores, overlap_scores, analysis_type, params, spatial_params,
spatial_patterns). Also adds @param lr_pairs on SpaceMarkers,
@param type on find_hotspots_gmm SME method, and @param object on the
show method for SpaceMarkersExperiment.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 7620749b550f100dc2aefb71c7f8779d0224bffa

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 13:25:18 -0400

      Commit message:


	  
		
 docs(vignette): rewrite SpaceMarkersStepByStep to use chainable SME API

Replaces the manual sme@spacemarkers\$results <- list(...) and
S4Vectors::metadata(sme)\$hotspots\$... <- hs assignments with a chain of
SME-in / SME-out method calls:

  sme_ud <- sme_ud |>
      find_all_hotspots() |>
      get_pairwise_interacting_genes(...) |>
      get_im_scores() |>
      calculate_overlap_undirected()

Setters (hotspots<-, interactions<-, undirected_scores<-, ...) are used
internally by the new SME dispatch methods, so user code no longer needs
to poke @spacemarkers or metadata() slots. The "Extracting Inputs from
the SME" section shrinks accordingly: the pipeline methods pull expr,
spPatterns, and optParams from the SME themselves. Vignette re-knitted
against the installed worktree build.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 1706061e500e3fbdf9100f4df1a0861360d5b155

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 13:16:51 -0400

      Commit message:


	  
		
 refactor(sme): dogfood SME pipeline methods inside OneSpaceMarkers helpers

Rewrites .undirected_SpaceMarkers_sme and .directed_SpaceMarkers_sme as
chains of the SME pipeline methods added in Tasks 2-12. Extracts the
barcode/gene filtering and spatial_params fallback from the legacy
.process_sme_input into a small .apply_sme_filters helper. Incidentally
fixes a pre-existing bug where calculate_gene_set_specificity was called
with the directed-scores data.frame instead of an expression matrix --
the new SME method uses the expression matrix correctly.

No behavior change for end users of SpaceMarkers(sme).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: bd07cf4351fc86969b4d533b7d054d41c82551c3

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 13:09:46 -0400

      Commit message:


	  
		
 feat(sme): calculate_lr_scores as S4 generic with SME method

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 49b34f86b0e9f8a9900375ab7ead9c1c24d4f7e1

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 13:04:02 -0400

      Commit message:


	  
		
 feat(sme): calculate_gene_set_specificity as S4 generic with SME method

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 4d2b09f5df3f736a020b8f4da753ee1c2fc945e8

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:51:05 -0400

      Commit message:


	  
		
 feat(sme): calculate_gene_set_score as S4 generic with SME method

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 39a885d956f86d0947eb6ecd8656191197f96f9f

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:45:47 -0400

      Commit message:


	  
		
 feat(sme): calculate_overlap_directed as S4 generic with SME method

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: b092dc3d0c4109a10a3fdf2d86aa14b842e666cf

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:43:30 -0400

      Commit message:


	  
		
 feat(sme): calculate_gene_scores_directed as S4 generic with SME method

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 92a076eb0e600de90ccb22ef02085e4bbd909e82

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:40:13 -0400

      Commit message:


	  
		
 feat(sme): find_hotspots_gmm as S4 generic with SME method and type dispatch

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 4746250860d86e9ec514b749ea67048cf4835c19

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:38:13 -0400

      Commit message:


	  
		
 feat(sme): calculate_influence as S4 generic with SME method

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: cb95005045549cb860297aca9419d65ad969773e

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:32:43 -0400

      Commit message:


	  
		
 fix(sme): restore pre-refactor find_all_hotspots default nullSamples = 1000

The plan and implementer accidentally dropped nullSamples from 1000 to 100
when promoting find_all_hotspots to an S4 generic. That is a behavior
change for every pre-existing caller that omitted the arg (10x less null
sampling, lower empirical p-value precision). Restores 1000 across the
generic, the data.frame default method, and the SpaceMarkersExperiment
method so back-compat is preserved.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 914995d0c6218640cae7a1a7f6fb99c6dd3d90d0

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:30:17 -0400

      Commit message:


	  
		
 feat(sme): calculate_overlap_undirected as S4 generic with SME method

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: b9568291890ead173c7b494866fc8e53d75b1af6

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:27:30 -0400

      Commit message:


	  
		
 feat(sme): get_im_scores as S4 generic with SME method

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 50e460003d47ee3e07ad20505d6e2cd802432584

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:24:53 -0400

      Commit message:


	  
		
 feat(sme): get_pairwise_interacting_genes as S4 generic with SME method

SME method reads expr, spPatterns, optParams, and hotspots(x,"undirected")
from the SME, runs the default method, and writes interactions(x) plus
params(x)\$mode, \$analysis_method, \$min_overlap.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 3f77e0ae1a17fe53ed7195e895233f2357d8fc3b

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:21:10 -0400

      Commit message:


	  
		
 feat(sme): find_all_hotspots as S4 generic with SME method

Existing data.frame behavior preserved as the default method; adds a
SpaceMarkersExperiment method that extracts spPatterns and params via
accessors, runs the default, and writes hotspots(sme, "undirected").

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 72512ed675afd2a3ec16c67897ab42ee175e4354

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:11:58 -0400

      Commit message:


	  
		
 chore: add man page for imports doc block

Generated by devtools::document() from the new @importFrom block added
in f27e346.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: f27e346c9ec84b0f94318477e172d59671c6bb3e

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:11:08 -0400

      Commit message:


	  
		
 fix(sme): delegate analysis_type<- to class validator; restore @importFrom

Replaces the hand-rolled enum check in analysis_type<- with
methods::validObject(x), so the valid-value list lives only in
setValidity (R/AllClasses.R). Adds a roxygen @importFrom block for
S4Vectors metadata/metadata<-, SummarizedExperiment assayNames/colData<-,
and methods setGeneric/validObject, restoring NAMESPACE entries that
were lost to devtools::document() on the first regeneration.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 11d6e40888e2881dda9e519197f06fb22f23ba62

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:03:01 -0400

      Commit message:


	  
		
 chore: regenerate man pages and Collate order

First devtools::document() run on this branch generated .Rd files for
the SME infrastructure added in 90c9b5e (SpaceMarkersExperiment class,
accessors, SpaceMarkers wrapper, load10X, etc.) and produced the roxygen
alphabetical Collate order. Content is derived from existing roxygen
tags; no source changes.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 012fdb630239c3414b237cff559f4ed0d58fdc99

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 12:01:08 -0400

      Commit message:


	  
		
 feat(sme): add setter generics and helpers for SpaceMarkersExperiment

Adds write-side generics (hotspots<-, interactions<-, influence_map<-,
undirected_scores<-, directed_scores<-, overlap_scores<-, lr_scores<-,
analysis_type<-) symmetric to the existing readers, plus unexported
helpers .sme_expr and .sme_spPatterns used by subsequent SME pipeline
methods. analysis_type<- enforces the valid value set.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: bceebb09fa7479d923e492fcdbd7cca79226c9ed

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 11:54:38 -0400

      Commit message:


	  
		
 docs: add implementation plan for SME pipeline methods

Breaks the design from the 2026-04-20 spec into 15 TDD tasks with exact
file paths, code, and commit messages. Each pipeline function is promoted
to an S4 generic in its own task, followed by vignette rewrite and
R CMD check.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: 90c9b5eae2743e25c3d8369683d057273c057ffe

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 11:45:44 -0400

      Commit message:


	  
		
 feat: add SpaceMarkersExperiment class and SME-aware infrastructure

Ports the uncommitted SME work from the keen-chatelet worktree so the
claude/sme-pipeline-methods branch can build on it. Includes the
SpaceMarkersExperiment S4 class (SpatialExperiment subclass with a
spacemarkers SimpleList slot), generics and accessors (hotspots,
interactions, undirected_scores, directed_scores, overlap_scores,
lr_scores, influence_map, spatial_patterns, spatial_params, params,
analysis_type), the SME-aware top-level SpaceMarkers() dispatcher in
OneSpaceMarkers.R, the SpaceMarkersExperiment and StepByStep vignettes,
and the accompanying testthat files. No behavior change for existing
file-path callers.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: f4b6f0398b5b17ceb3246c4f98c7fb6a5acd7341

      Author:  adeshpa6 <atulpdeshpande@gmail.com> 

      Date: 2026-04-20 11:41:19 -0400

      Commit message:


	  
		
 docs: add design spec for SME pipeline methods

Adds docs/superpowers/specs/2026-04-20-sme-pipeline-methods-design.md
describing setter generics symmetric to each result reader and SME-dispatch
methods for every per-step pipeline function, so the step-by-step vignette
can chain SME-in/SME-out calls instead of poking slots directly.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: SpaceMarkers

      Commit: f55d3f9adbb23f7363b44bbb12a61662cb7f387d

      Author:  orian116 <ostaple1@jhu.edu> 

      Date: 2026-03-09 15:26:25 -0400

      Commit message:


	  
		
 Added SpaceMarkers wrapper function R folder as OneSpaceMarkers.R. This was created from Dima's SpaceMarkers.R function in the dispatch branch and modified to be compatibile with the main branch including a generalized function to process inputs. Removed extra ellipsis
 
    
  
    

      Package: SpaceMarkers

      Commit: 6872be820696b44d792e36db6c3ecff482bdfc18

      Author:  orian116 <ostaple1@jhu.edu> 

      Date: 2026-03-09 15:25:15 -0400

      Commit message:


	  
		
 Added SpaceMarkers wrapper function R folder as OneSpaceMarkers.R. This was created from Dima's SpaceMarkers.R function in the dispatch branch and modified to be compatibile with the main branch including a generalized function to process inputs
 
    
  
    

      Package: SpaceMarkers

      Commit: 07b53c68bd5e070c5b76ff374859244cda1d369b

      Author:  dimalvovs <dmitrijs.lvovs@gmail.com> 

      Date: 2025-12-19 12:57:01 -0500

      Commit message:


	  
		
 fix input, close #87 (#88)

* fix input, close #87

* harmonize outputs (just csv to rds)

* Update nextflow/main.nf

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* rename to IMscores

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 
    
  
    

      Package: SpaceMarkers

      Commit: ead294d01081609773f6c055ecdbadf1cfe0f772

      Author:  dimalvovs <dmitrijs.lvovs@gmail.com> 

      Date: 2025-11-11 10:07:16 -0500

      Commit message:


	  
		
 fix pipeline (#84)

* fix function names

* make optional lrscores

* add nextflow params

* using the right hotspots

---------

Co-authored-by: adeshpa6 <atulpdeshpande@gmail.com> 
    
  
    

      Package: SpaceMarkers

      Commit: 9fd1a2c086fb63798fd916248eca41de25761713

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2025-11-06 14:03:01 -0500

      Commit message:


	  
		
 Merge pull request #83 from DeshpandeLab/nextflow

Nextflow 
    
  
    

      Package: SpaceMarkers

      Commit: ce907ca4589d1e38d86e7bef65e6cc9ea6c8e8dd

      Author:  dimalvovs <dmitrijs.lvovs@gmail.com> 

      Date: 2025-11-06 12:54:42 -0500

      Commit message:


	  
		
 add libglpk
 
    
  
    

      Package: SpaceMarkers

      Commit: 393eff16555dccd232db263d445267562a1154f5

      Author:  dimalvovs <dmitrijs.lvovs@gmail.com> 

      Date: 2025-11-06 12:31:01 -0500

      Commit message:


	  
		
 debug
 
    
  
    

      Package: SpaceMarkers

      Commit: 28c903f966fd26309be64cef06a4638fbe6d5789

      Author:  dimalvovs <dmitrijs.lvovs@gmail.com> 

      Date: 2025-11-06 12:17:04 -0500

      Commit message:


	  
		
 add Bioc dependency for CellChat
 
    
  
    

      Package: SpaceMarkers

      Commit: 4b7d3ae9348b376996848ac52395b9c74bbd7524

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2025-11-06 11:01:42 -0500

      Commit message:


	  
		
 Merge pull request #82 from DeshpandeLab/nextflow

add CellChat dependency 
    
  
    

      Package: SpaceMarkers

      Commit: ece1a335ca1d88c2d4319481f4a2292ea65b8309

      Author:  dimalvovs <dmitrijs.lvovs@gmail.com> 

      Date: 2025-11-05 16:50:46 -0500

      Commit message:


	  
		
 add CellChat dependency
 
    
  
    

      Package: SpaceMarkers

      Commit: 0029c3883c70e3c2d580389bd79e1afb3bba0c27

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2025-11-05 13:00:51 -0500

      Commit message:


	  
		
 Merge pull request #81 from DeshpandeLab/bioc

Bioconductor sync 
    
  
    

      Package: SpaceMarkers

      Commit: 191fa7e254f1aad5f2bf2eb94ec186d30749235a

      Author:  dimalvovs <dmitrijs.lvovs@gmail.com> 

      Date: 2025-11-05 11:47:53 -0500

      Commit message:


	  
		
 Merge branch 'main' of github.com:DeshpandeLab/SpaceMarkers
 
    
  
    

      Package: SpaceMarkers

      Commit: ee4377c124058d890b6e5aeece7d532301d4cd46

      Author:  atuldeshpande <adeshpande@jhu.edu> 

      Date: 2025-10-27 13:11:32 -0400

      Commit message:


	  
		
 Merge pull request #80 from DeshpandeLab/merge_upstream

Merge upstream 
    
  
    

      Package: S4Vectors

      Commit: 4180a7b4f17a5ace243b59dad013efcdb6a0e659

      Author:  Michael Lawrence <lawremi@gmail.com> 

      Date: 2026-04-28 20:39:16 -0700

      Commit message:


	  
		
 top_prenv_dots() supports unnamed args again (used by rsolr)
 
    
  
    

      Package: cellNexus

      Commit: 7d120c7213adb69d65d946df5ff8091bbc4e3b10

      Author:  Mengyuan Shen <129487421+myushen@users.noreply.github.com> 

      Date: 2026-04-29 12:43:58 +1000

      Commit message:


	  
		
 Merge pull request #108 from myushen/master

fix vignette logo path 
    
  
    

      Package: cellNexus

      Commit: 56f717b06fba8362a18466f50efd54c3a74e4e9b

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-29 12:21:05 +1000

      Commit message:


	  
		
 csl logo
 
    
  
    

      Package: cellNexus

      Commit: 96bc4f034510396384d116c4c1c256037ccb6dbc

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-29 12:00:06 +1000

      Commit message:


	  
		
 fix vignette logo path
 
    
  
    

      Package: cellNexus

      Commit: 23642601dc72b79a7981ee97927048f0e319255b

      Author:  Mengyuan Shen <129487421+myushen@users.noreply.github.com> 

      Date: 2026-04-29 11:07:55 +1000

      Commit message:


	  
		
 Merge pull request #106 from Bisaloo/review-take2

Misc review fixes 
    
  
    

      Package: cellNexus

      Commit: 89419be6ea46097604a27a1b14a8ae51e7260fd6

      Author:  Mengyuan Shen <129487421+myushen@users.noreply.github.com> 

      Date: 2026-04-29 11:05:52 +1000

      Commit message:


	  
		
 Merge branch 'master' into review-take2 
    
  
    

      Package: cellNexus

      Commit: c83092994375982f588f6d61c1c06cea52e336c0

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-29 11:01:39 +1000

      Commit message:


	  
		
 write precompute for all vignettes/ Rmds
 
    
  
    

      Package: cellNexus

      Commit: c33a19c4184734633c8079209d69fa4ebb354d92

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-28 19:34:57 +1000

      Commit message:


	  
		
 move unused future functions in R/ folder to dev.R
 
    
  
    

      Package: cellNexus

      Commit: 20071f3bb469bb4ff16f4d4f2886e63773729438

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-04-28 17:38:53 +0930

      Commit message:


	  
		
 Merge pull request #107 from MangiolaLaboratory/add-CSL-logo

Add csl logo 
    
  
    

      Package: cellNexus

      Commit: b8487903db36cff8ee28076f972ab852eae9933c

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-04-28 17:38:14 +0930

      Commit message:


	  
		
 Update README.md 
    
  
    

      Package: cellNexus

      Commit: 5f3c3627dbfad7e8dff971d371eab286edff539d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-04-28 17:37:38 +0930

      Commit message:


	  
		
 Fix logo image tags in README.md 
    
  
    

      Package: cellNexus

      Commit: 6359afd4c97ac5d34e7024cc78984c8c3dc1c8a1

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-04-28 17:37:08 +0930

      Commit message:


	  
		
 Update logos in README.md 
    
  
    

      Package: cellNexus

      Commit: 5f7c54918d62cfb3900b165c88b06f211eb300c3

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-04-28 17:36:26 +0930

      Commit message:


	  
		
 Add files via upload 
    
  
    

      Package: cellNexus

      Commit: 8d9b2f33135c4b00b09b7da6ae9136634b72481d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-04-28 17:35:22 +0930

      Commit message:


	  
		
 Fix typos and enhance README

Corrected typos and improved clarity in the README. 
    
  
    

      Package: cellNexus

      Commit: 1fa12e90b16fe42cfc825911ce899e727114f3c3

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-04-28 17:32:08 +0930

      Commit message:


	  
		
 Change license to GPL-2.0 (GNU GPL v2 text) 
    
  
    

      Package: cellNexus

      Commit: c0992500fd1b0e31fb0024b6227a926417b90e94

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-04-28 17:21:02 +0930

      Commit message:


	  
		
 Update README.md 
    
  
    

      Package: cellNexus

      Commit: bf6f40669e9e44f7fff7e886614222e48573f2be

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-28 17:47:33 +1000

      Commit message:


	  
		
 precompute package vignettes
 
    
  
    

      Package: cellNexus

      Commit: bd2a9905b3fe8722c7ee1aeb002f35d8188764b3

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-27 10:35:51 +0200

      Commit message:


	  
		
 Add fct markup in vignette
 
    
  
    

      Package: cellNexus

      Commit: bd49ef50c095fd01496046401702715304c9dadf

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-27 10:00:30 +0200

      Commit message:


	  
		
 Use expected extension on NEWS file
 
    
  
    

      Package: cellNexus

      Commit: c49d8256c0ad54c28019672b654c68f96d44d9b1

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-17 19:19:01 +0200

      Commit message:


	  
		
 Use && where relevant
 
    
  
    

      Package: cellNexus

      Commit: dbaa43d23e5da387ce92468fbfe2e534e32797ee

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-17 19:18:19 +0200

      Commit message:


	  
		
 Avoid == TRUE/FALSE
 
    
  
    

      Package: cellNexus

      Commit: 278bb2eb52d74450c830cdbfdee136007dd3a2cb

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-17 19:17:45 +0200

      Commit message:


	  
		
 Do not use deprecated function in CITATION
 
    
  
    

      Package: cellNexus

      Commit: 68fdf94c6c153b727bacddf9d517abd4ad657a43

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-17 19:17:28 +0200

      Commit message:


	  
		
 Remove NEWS.md

Redundant with inst/NEWS.Rd
 
    
  
    

      Package: cellNexus

      Commit: 7e19a7631b3e607d5aa47b0ff7481df0c6c8ed7f

      Author:  Mengyuan Shen <129487421+myushen@users.noreply.github.com> 

      Date: 2026-04-24 21:24:52 +1000

      Commit message:


	  
		
 Merge pull request #103 from myushen/syntax_and_docs

Fix metadata consistency and update annotation documentation 
    
  
    

      Package: cellNexus

      Commit: 456a4b15ed672836066fdb98a2b6b916cfcdeb54

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-21 14:01:14 +1000

      Commit message:


	  
		
 fix metadata consistency with pseudobulk. update annotation documentation
 
    
  
    

      Package: cellNexus

      Commit: 27fb1670814e16812abee0ee34b3a83640290078

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-21 09:57:29 +1000

      Commit message:


	  
		
 Merge branch 'master' into syntax_and_docs
merge from master
 
    
  
    

      Package: cellNexus

      Commit: 05f3426d5603b78da00c7ba001a63e293708007f

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-17 17:23:02 +1000

      Commit message:


	  
		
 metadata documentation
 
    
  
    

      Package: cellNexus

      Commit: 8b6f18e9480917375a45a802fee84c097287ea06

      Author:  Mengyuan Shen <129487421+myushen@users.noreply.github.com> 

      Date: 2026-04-17 13:59:59 +1000

      Commit message:


	  
		
 Merge pull request #102 from myushen/syntax_and_docs

Update documentation and address Check notes 
    
  
    

      Package: cellNexus

      Commit: fc8e40022dd4ac8625b7f6f769b077bba0d447f1

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-17 12:47:10 +1000

      Commit message:


	  
		
 update pseudobulk example
 
    
  
    

      Package: cellNexus

      Commit: 6727fe92ef48480afc1a8932f94429624b5c8be2

      Author:  Mengyuan Shen <mengyuan.shen@outlook.com> 

      Date: 2026-04-16 17:29:13 +1000

      Commit message:


	  
		
 try again
 
    
  
    

      Package: cellNexus

      Commit: 39dafd6d75f1253500dc4ad9ea71b8405b8b7a48

      Author:  Mengyuan Shen <mengyuan.shen@outlook.com> 

      Date: 2026-04-16 17:06:23 +1000

      Commit message:


	  
		
 manifest staled
 
    
  
    

      Package: cellNexus

      Commit: 4dc5a20ee4e37ffea686f74adf888808addce9e7

      Author:  Mengyuan Shen <mengyuan.shen@outlook.com> 

      Date: 2026-04-16 16:52:03 +1000

      Commit message:


	  
		
 renv.lock fetch from bioc
 
    
  
    

      Package: cellNexus

      Commit: 706e3a456aff42f72c87ec7778eb74c9ac71d39f

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-16 16:36:50 +1000

      Commit message:


	  
		
 renv.lock
 
    
  
    

      Package: cellNexus

      Commit: 397ec032c0d211a20b9997caadfd22f3e6bd6335

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-16 14:23:07 +1000

      Commit message:


	  
		
 renv.lock
 
    
  
    

      Package: cellNexus

      Commit: 06a205d8bf2a75f2153143cb19d8ebe4f685b8ed

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-16 14:05:45 +1000

      Commit message:


	  
		
 undocument join_census. update style
 
    
  
    

      Package: cellNexus

      Commit: 11b1723e0c65c3d17d7cf393e09f33dab03bb3fa

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-16 12:07:30 +1000

      Commit message:


	  
		
 sample metadata, and vignettes
 
    
  
    

      Package: cellNexus

      Commit: 31ae2c693db96c4c84441580ca7b8e10100d882e

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-15 18:07:30 +1000

      Commit message:


	  
		
 documentation
 
    
  
    

      Package: cellNexus

      Commit: 91e08858df246c4636d31c0d199c128767d1b192

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-15 15:00:22 +1000

      Commit message:


	  
		
 add cell communication demo to vignette
 
    
  
    

      Package: cellNexus

      Commit: b53534ba9c3783fd53778f616906c7fe7878a4d4

      Author:  myushen <mengyuan.shen@outlook.com> 

      Date: 2026-04-15 10:09:25 +1000

      Commit message:


	  
		
 split sample metadata to cellnexus and census
address bioccheck note
 
    
  
    

      Package: cellNexus

      Commit: d7efbcfc644fffd727ef7e1d3861d37f801002f8

      Author:  Mengyuan Shen <mengyuan.shen@outlook.com> 

      Date: 2026-04-14 16:38:58 +1000

      Commit message:


	  
		
 address R CMD check notes
 
    
  
    

      Package: BenchHub

      Commit: 7f702ca89fc07193d8369245b73d2fe4bbec1968

      Author:  Dario Strbenac <dario@maths.usyd.edu.au> 

      Date: 2026-04-29 13:20:16 +1000

      Commit message:


	  
		
 Increased version for Cabiria's changes.
 
    
  
    

      Package: BenchHub

      Commit: 5405f2df28eb0add774281f6f3b6018c2990aabc

      Author:  littlecabiria <71769896+littlecabiria@users.noreply.github.com> 

      Date: 2026-04-28 11:14:28 +1000

      Commit message:


	  
		
 upload example
 
    
  
    

      Package: BenchHub

      Commit: ab46c60626071d5801067bb70b3c72e4ae968550

      Author:  Yue Cao <yue.cao@sydney.edu.au> 

      Date: 2026-04-23 12:02:28 +1000

      Commit message:


	  
		
 remove suppress warnings
 
    
  
    

      Package: BenchHub

      Commit: d5b64e530ce19e806fc1a50d6cf4b5e4bb9a296f

      Author:  Yue Cao <yue.cao@sydney.edu.au> 

      Date: 2026-04-23 11:55:33 +1000

      Commit message:


	  
		
 label code chunk for figures
 
    
  
    

      Package: BenchHub

      Commit: 859f43df40d205af62b9fcf06851a03d616a59f1

      Author:  Yue Cao <yue.cao@sydney.edu.au> 

      Date: 2026-04-23 11:50:11 +1000

      Commit message:


	  
		
 update rd
 
    
  
    

      Package: BenchHub

      Commit: ddaeaa8cc4ff6fedbc0ac89a756e742041458099

      Author:  Yue Cao <yue.cao.au@gmail.com> 

      Date: 2026-04-23 11:36:58 +1000

      Commit message:


	  
		
 add example to downloadsubmissionstudy function 
    
  
    

      Package: BenchHub

      Commit: 5131d6c341bc36b660983ab4e6d7e913e3c57b86

      Author:  Yue Cao <yue.cao.au@gmail.com> 

      Date: 2026-04-23 11:26:39 +1000

      Commit message:


	  
		
 label code chunks 
    
  
    

      Package: BenchHub

      Commit: 526161e654315cd1d387105d6c4d45fe20ba4f00

      Author:  Yue Cao <yue.cao.au@gmail.com> 

      Date: 2026-04-23 11:24:24 +1000

      Commit message:


	  
		
 label code chunks 
    
  
    

      Package: BenchHub

      Commit: 7c1fb1a6fd2f4a2a1868ec7c30f916b6a003f33f

      Author:  Yue Cao <yue.cao.au@gmail.com> 

      Date: 2026-04-23 11:23:29 +1000

      Commit message:


	  
		
 label code chunks 
    
  
    

      Package: BenchHub

      Commit: 7dde0bf2773cef4a6f336c792e4b54f7f733d44a

      Author:  Yue Cao <yue.cao.au@gmail.com> 

      Date: 2026-04-23 11:21:36 +1000

      Commit message:


	  
		
 label code chunks 
    
  
    

      Package: BenchHub

      Commit: 8b6ed21121df1b2e7ddbecbb80732b02cdf4c6c3

      Author:  Yue Cao <yue.cao.au@gmail.com> 

      Date: 2026-04-23 11:19:49 +1000

      Commit message:


	  
		
 label code chunks 
    
  
    

      Package: BenchHub

      Commit: efc7f0b82b21c2bff756ac69381af38862dd3efc

      Author:  Yue Cao <yue.cao.au@gmail.com> 

      Date: 2026-04-23 11:00:23 +1000

      Commit message:


	  
		
 replace dontrun with if( interactive)

Updated example section to include interactive check. 
    
  
    

      Package: BenchHub

      Commit: 1f74335f2b2e7dbe44ce0faf928762d92211bfc1

      Author:  Yue Cao <yue.cao.au@gmail.com> 

      Date: 2026-04-23 10:28:54 +1000

      Commit message:


	  
		
 use googlesheet native quiet mode to replace suppressmessage 
    
  
    

      Package: BenchHub

      Commit: 4c35c6a0c128212345120de0d82a41ae5648ddd8

      Author:  Yue Cao <yue.cao.au@gmail.com> 

      Date: 2026-04-23 10:26:51 +1000

      Commit message:


	  
		
 use googlesheet native quiet mode to replace suppressmessage 
    
  
    

      Package: BenchHub

      Commit: 5b0b033baad471b9f86f96a3ff0685c85c223360

      Author:  Yue Cao <yue.cao.au@gmail.com> 

      Date: 2026-04-23 10:23:29 +1000

      Commit message:


	  
		
 remove suppress warnings 
    
  
    

      Package: BenchHub

      Commit: b47c5ce57ac220518c5dbf30bf3f33ae25bc03cd

      Author:  Yue Cao <yue.cao.au@gmail.com> 

      Date: 2026-04-23 10:17:32 +1000

      Commit message:


	  
		
 remove warnings 
    
  
    

      Package: BenchHub

      Commit: 30ff964546291ad7df48bb6708442d521f9815db

      Author:  Yue Cao <yue.cao.au@gmail.com> 

      Date: 2026-04-23 09:17:45 +1000

      Commit message:


	  
		
 remove paste in message 
    
  
    

      Package: BenchHub

      Commit: fb0a49884c6b5d2f789e00cc2340864d5155274b

      Author:  Dario Strbenac <dario@maths.usyd.edu.au> 

      Date: 2026-04-23 06:00:11 +1000

      Commit message:


	  
		
 Add (untracked since January) NEWS.Rd file and increase R version dependency.
 
    
  
    

      Package: scPipe

      Commit: 4a4ba6ba8f0419a3b3a948c73bcd3813471fc58f

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-04-29 11:54:35 +1000

      Commit message:


	  
		
 Merge branch 'devel' of git.bioconductor.org:packages/scPipe into devel
 
    
  
    

      Package: scPipe

      Commit: ac50a95449f55c16601d81acaef95d2c20d32de1

      Author:  shians <registertonysu@gmail.com> 

      Date: 2026-04-29 11:54:15 +1000

      Commit message:


	  
		
 Update CITATION
 
    
  
    

      Package: OrganismDbi

      Commit: 9880605db7788f84d1e6c33458ab94d4ff1cbcb6

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-04-28 16:43:10 -0700

      Commit message:


	  
		
 OrganismDbi 1.55.1: Drop arguments 'url' and 'port'

These were deprecated in BioC 3.22 and defunct in BioC 3.23.
 
    
  
    

      Package: Biobase

      Commit: c1f775a5db43b9f30fe5fb71ef2d60cc3ca851b9

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-04-28 15:51:49 -0700

      Commit message:


	  
		
 Biobase 2.73.1: Get rid of stuff that has been defunct for 10+ years

This includes things like classes exprSet, phenoData, and annotatedDataset,
or the l2e() function, etc...
 
    
  
    

      Package: BiocIO

      Commit: 145536de8f8d3c75c341455abc4e83191be6cc04

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-28 18:14:47 -0400

      Commit message:


	  
		
 version bump 1.23.3
 
    
  
    

      Package: BiocIO

      Commit: d10dcb920e5577d132d9c03d1b30bb75b2e28e15

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-28 18:14:42 -0400

      Commit message:


	  
		
 add hosts in unit tests
 
    
  
    

      Package: BiocIO

      Commit: d1dc3913fc785cf8bdf6c5e9c9e9660040ccadb6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-28 18:14:19 -0400

      Commit message:


	  
		
 combine host and path for file schemes
 
    
  
    

      Package: BiocIO

      Commit: 216a09ac975867f16b0cc7bea62aef6a7ed8da04

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-28 17:51:17 -0400

      Commit message:


	  
		
 version bump 1.23.2
 
    
  
    

      Package: BiocIO

      Commit: 0d1d481f3b8a44089cee7c07e3a2075cb054db6f

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-28 17:51:09 -0400

      Commit message:


	  
		
 simplify .parseURI

Assisted-by: claude-sonnet-4-6
 
    
  
    

      Package: BiocIO

      Commit: 6a69d72a8ff2b7edc441b226ae3a5cbfa2631af8

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-28 17:26:09 -0400

      Commit message:


	  
		
 version bump 1.23.1
 
    
  
    

      Package: BiocIO

      Commit: 74d930a9feec3fabf7a3bb31d83bf64f74294092

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-28 17:26:03 -0400

      Commit message:


	  
		
 update RoxygenNote 7.3.3
 
    
  
    

      Package: BiocIO

      Commit: eca2daa5984c8a521f06f115b9afc91ccefcd24b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-28 17:25:52 -0400

      Commit message:


	  
		
 import BiocBaseUtils isScalarCharacter
 
    
  
    

      Package: BiocIO

      Commit: fe53135558339c5e5f9456f1323d22ed2eef877b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-28 17:25:33 -0400

      Commit message:


	  
		
 error when missing format for text import
 
    
  
    

      Package: BiocIO

      Commit: e48e7138cd9a5e1543e24953f768dbcee3d98709

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-28 17:25:16 -0400

      Commit message:


	  
		
 use double bracket instead of $ for extraction
 
    
  
    

      Package: BiocIO

      Commit: 91741000f05a495f8676dd1ab491097da1883ad6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-28 17:24:48 -0400

      Commit message:


	  
		
 use named character vector throughout for method signatures
 
    
  
    

      Package: PIPETS

      Commit: 10d2b25c471641c5b135656ba611e3b49be113ce

      Author:  qfurumo <furumq@gmail.com> 

      Date: 2026-04-28 15:55:03 -0400

      Commit message:


	  
		
 Updating author description fields
 
    
  
    

      Package: PIPETS

      Commit: e88fed0d2084281833f146f9713b27d7845152a5

      Author:  qfurumo <furumq@gmail.com> 

      Date: 2026-04-28 15:21:12 -0400

      Commit message:


	  
		
 Updating maintainer
 
    
  
    

      Package: PIPETS

      Commit: bfd52bfb6c7df90b8407bade3f02be68440dea24

      Author:  qfurumo <furumq@gmail.com> 

      Date: 2026-04-28 14:48:45 -0400

      Commit message:


	  
		
 Updating Version Number to match upstream

Merge branch 'devel' of git.bioconductor.org:packages/PIPETS into devel

# Conflicts:
#	DESCRIPTION
 
    
  
    

      Package: PIPETS

      Commit: 730a82ace355a52cf98d94bbca8a6f015f55c736

      Author:  qfurumo <furumq@gmail.com> 

      Date: 2025-06-12 16:47:11 -0400

      Commit message:


	  
		
 Version bump and lowered minumum number of columns to 5.
 
    
  
    

      Package: PIPETS

      Commit: 10baa8f215d64295f65c3b6cfd79c7940b13b843

      Author:  qfurumo <furumq@gmail.com> 

      Date: 2025-01-08 13:04:21 -0500

      Commit message:


	  
		
 Version Bump For Post Bioconductor 3.20 change
 
    
  
    

      Package: carnation

      Commit: 4789c1f5fd2ca0228212e8dceeacd2166fcaee06

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-04-28 14:04:36 -0400

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel' into devel
 
    
  
    

      Package: carnation

      Commit: 17873cf5c74bf20a5009bf682db9fc417ee44286

      Author:  Apratim Mitra <16709900+mitraak@users.noreply.github.com> 

      Date: 2026-04-28 13:36:44 -0400

      Commit message:


	  
		
 Merge pull request #32 from NICHD-BSPC/main

Merge main into devel 
    
  
    

      Package: bettr

      Commit: 72774f7cd06b686037a0486484783110e688fb04

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-04-28 19:30:56 +0200

      Commit message:


	  
		
 Fix merge conflict

Merge remote-tracking branch 'upstream/devel' into devel

# Conflicts:
#	DESCRIPTION
 
    
  
    

      Package: bettr

      Commit: 607f1f557ad47b03af7e8c19780bba9e1548efb3

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-04-04 14:12:46 +0200

      Commit message:


	  
		
 Merge pull request #29 from federicomarini/expand-readme

Expand README, move highlight method UI to parallel coordinates tab 
    
  
    

      Package: bettr

      Commit: 1aaf37bfa74542bed16e71b39b2c5d7883622b39

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-04-04 13:51:19 +0200

      Commit message:


	  
		
 Move highlightMethodUI to the parallel coordinates tab, allow multiple selected values
 
    
  
    

      Package: bettr

      Commit: 37d273e85c9aed48d34ec52963be83756e77696b

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-04-04 13:33:02 +0200

      Commit message:


	  
		
 Add quick links section to README
 
    
  
    

      Package: bettr

      Commit: b798083a5952ee1cc4f5959464bf3bf7b4d90eb6

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-04-04 13:30:44 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: bettr

      Commit: 8d692c313afcb3b8763e26ac12f9073f0dbd9d9a

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2026-03-21 10:48:24 +0100

      Commit message:


	  
		
 Bump cache version
 
    
  
    

      Package: bettr

      Commit: 07201a26bf3b7a14c0097e28e29715d4a48bbd07

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2025-11-29 18:22:38 +0100

      Commit message:


	  
		
 Update GHA cache version, add _pkgdown.yml
 
    
  
    

      Package: arrayQualityMetrics

      Commit: 282fcaa83dfc53c1a7aa012ab813eedb44eb6181

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 19:28:11 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: arrayQualityMetrics

      Commit: e8ce3888931fb941188670856f337390a3a9b35d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 19:28:02 +0200

      Commit message:


	  
		
 Mention RColorBrewer removal in NEWS
 
    
  
    

      Package: arrayQualityMetrics

      Commit: 0ea81b662d1528b69a9d503025f39efaf99013f3

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-21 11:37:12 +0200

      Commit message:


	  
		
 Replace RColorBrewer by grDevices
 
    
  
    

      Package: arrayQualityMetrics

      Commit: 8d1bfe8f80201509e6483d617f3f8989590cbc45

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-28 10:48:13 +0200

      Commit message:


	  
		
 Remove travis and use GitHub Actions
 
    
  
    

      Package: universalmotif

      Commit: f906eda6c35cca897d038e1548360be46acf6999

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-04-28 16:16:53 +0100

      Commit message:


	  
		
 v1.30.1 bugfix version bump
 
    
  
    

      Package: universalmotif

      Commit: 90d0c9c55c758d740c20a2e12b96b040d608ad3c

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-04-28 16:14:26 +0100

      Commit message:


	  
		
 Merge branch 'temp-bugfixes'
 
    
  
    

      Package: universalmotif

      Commit: ca2a564b0498c6b16bfd058f736bd35b899ca278

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-04-28 10:35:40 +0100

      Commit message:


	  
		
 another round of bugfixes
 
    
  
    

      Package: universalmotif

      Commit: 4c8b139e9077092cdfecf2e3c5809367115d37bd

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-04-28 09:31:47 +0100

      Commit message:


	  
		
 more tests
 
    
  
    

      Package: universalmotif

      Commit: 64325bd564885aaa6e1fb23206adb5c1fc7d0a14

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-04-27 21:35:30 +0100

      Commit message:


	  
		
 amend vignette per the bugfix
 
    
  
    

      Package: universalmotif

      Commit: 2bcfb77b6553add1a377029ed4774b2b77c290b3

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-04-27 21:27:20 +0100

      Commit message:


	  
		
 more bugfixes from cc
 
    
  
    

      Package: universalmotif

      Commit: cc0ea6d0aaef4a300e591431010b2e5325bbf5e5

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-04-27 15:34:39 +0100

      Commit message:


	  
		
 more memory savings
 
    
  
    

      Package: universalmotif

      Commit: fe5b8339e765fbbb207be5375ad4579802716719

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-04-27 14:54:44 +0100

      Commit message:


	  
		
 improve memory usage in scan_sequences
 
    
  
    

      Package: universalmotif

      Commit: e8ab7e220b929d00640fd5056cbb9760546565cc

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-04-27 14:31:27 +0100

      Commit message:


	  
		
 lots of bugfixes from cc
 
    
  
    

      Package: GOaGO

      Commit: 5450f5739708ed72a931ab0556c6490d76127707

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:20 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: GOaGO

      Commit: ace0eb8d032c2f8f769deb5408704797a872fc35

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:20 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: ClonalSim

      Commit: 6048f4bf99d8d4830dcc714f9cf298ed72c22269

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:19 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: ClonalSim

      Commit: fb76c2bd93849c50ffc42e8c0a51a966712dc647

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:19 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: queeems

      Commit: 54d1ec1b37ed1e581a5b410e73cbefc218e9df26

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:17 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: queeems

      Commit: c33f2089d26db47476a442545c68d5f78ebdc458

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:17 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: metabom8

      Commit: 977c8fa65f3cf4e93f307b22638727f28cc7114c

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:17 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: metabom8

      Commit: f18c26072e9ed2aa4a97644e8994c7e27f46568f

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:16 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: ImageArray

      Commit: 052d69dbe0e08b5dc1c3a8baf4c80178411d353f

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:16 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: ImageArray

      Commit: d0b205d05a542d35a0e2ae4b11cc323e62a36151

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:16 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: BatChef

      Commit: b4ef68ead2bdbffe5c68c9161311fd3a1d5fcfa2

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:15 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: BatChef

      Commit: 95632732369ffd58a8086fef2673a200d7c8c7ef

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:15 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: lncRna

      Commit: ae94230cbb791cb2e13b18e9e8555f7a054f1ebc

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:14 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: lncRna

      Commit: ad4cf2f3f87ad5c0d312561436d4ad39ee11bc3d

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:14 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: wavFeatExt

      Commit: 62f26cb7ae4946b720e082819bfad3ac9ed73a3d

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:13 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: wavFeatExt

      Commit: 6656f3d4e4bfec710bcc242d7d6f411096c36fe4

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:13 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: atacInferCnv

      Commit: 0347acd24dadb5847dbca2f409b4249a21b61249

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:12 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: atacInferCnv

      Commit: e1f67737db098e895ab696ee0bf5825c829cd081

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:12 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: immLynx

      Commit: f5adcfcc1c2acd3b466125d6ec5651ddecd255f6

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:11 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: immLynx

      Commit: e2fd5794bff0b71d8be08f0154e75395c2262b4a

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:11 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: epiRomics

      Commit: 9e2708e0bdd1934dffc2554020555520d5835958

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:10 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: epiRomics

      Commit: 7332a8dcfe59de4eb29874aa6294387bd18c1b2d

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:10 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: GraphExperiment

      Commit: 45c7264444d78f2ef176beff028678d05ed431df

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:08 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: GraphExperiment

      Commit: 6eaa004edd55b31597e120a16fa120468e036738

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:08 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: BiocAzul

      Commit: 7c7d7dd3b37f662abcdc8405671f2aab0b269d74

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:08 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: BiocAzul

      Commit: a9d670f9fe52964c8283e00b8b26ec7f236ee697

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:07 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: splicelogic

      Commit: 3db43b20af1c7799cf33b9d5ea49796d8b5b147c

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:07 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: splicelogic

      Commit: 4fb9961fe7abd7da084090a7aee5cf48f7018aa8

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:07 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: HistoImagePlot

      Commit: 412ed9b62c68ae8ed2ad10c720c51c3370de2f70

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:06 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: HistoImagePlot

      Commit: af4dcb1b959fa6f1f19c2ee0523204620e457680

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:06 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: imageFeatureTCGA

      Commit: fbc4a75c43406530ef86d85a73ac0f74401b14fa

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:05 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: imageFeatureTCGA

      Commit: 39ba8ff843dd3b09f910453b47d36b7b95330cee

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:05 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: scToppR

      Commit: c7f53065cb88988f6bf0fafce59ce88948bf0010

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:04 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: scToppR

      Commit: 9569ca01eb5e5c2d0753f9f2638890f6422749d3

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:04 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: CrcBiomeScreen

      Commit: ad84731c505db4e5bb0d0d6048096ab446d07314

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:03 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: CrcBiomeScreen

      Commit: fa65626d532a18e18ac8fc37a07934b3d3980d9d

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:03 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: postNet

      Commit: 6b1e4b68bdf3ead80fe0a467742282932bb36f1a

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:03 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: postNet

      Commit: 7f826932bc7a5d6ae6e7dd5dab7a4dd8bfb07865

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:03 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: scECODA

      Commit: 852992caf392f8354d8c1c079e016f0ae59116de

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:02 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: scECODA

      Commit: 7eb703af84625cbe3e23ff536f29c5d589bcbc4e

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:02 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: VISTA

      Commit: ea087d427e11c7468c8b1f0a38b5ab9bb26c8f22

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:01 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: VISTA

      Commit: d7e91e75f34dc308af5d1536a452fad9707ad2fa

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:01 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: imageTCGAutils

      Commit: b2293e7a1340d4813c75fd4e73ab7a300f633e65

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:00 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: imageTCGAutils

      Commit: 40b6a03d18f466db0c764b7c3d448f0e9412b1e5

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:07:00 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: fastRanges

      Commit: a9dee34d4e4459a83b13b6b3d5d9f23fde07bb55

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:59 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: fastRanges

      Commit: 36a6c0584023ea09bf650aae2f9101991941cc4a

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:59 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: PlinkMatrix

      Commit: bfa6bf024320391550fbb2445069b7ce809247a4

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:58 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: PlinkMatrix

      Commit: a78a4978eeeb256b13cf50d7aac50f2e164d8692

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:58 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: Rega

      Commit: 10c7dbc628224ceb8761dc1cd23f9af3e313cc3b

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:58 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: Rega

      Commit: 5a605727f75716462dc3eb023669e89de8b14cc9

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:57 -0400

      Commit message:


	  
		
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      Package: parati

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:57 -0400

      Commit message:


	  
		
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      Package: parati

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:57 -0400

      Commit message:


	  
		
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      Package: scTypeEval

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:56 -0400

      Commit message:


	  
		
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      Package: scTypeEval

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:56 -0400

      Commit message:


	  
		
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      Package: RankMap

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:55 -0400

      Commit message:


	  
		
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      Package: RankMap

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:55 -0400

      Commit message:


	  
		
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      Package: betterChromVAR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:54 -0400

      Commit message:


	  
		
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      Package: betterChromVAR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:54 -0400

      Commit message:


	  
		
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      Package: LRDE

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:53 -0400

      Commit message:


	  
		
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      Package: LRDE

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:53 -0400

      Commit message:


	  
		
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      Package: scLang

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:53 -0400

      Commit message:


	  
		
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      Package: scLang

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:53 -0400

      Commit message:


	  
		
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      Package: GSABenchmark

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:52 -0400

      Commit message:


	  
		
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      Package: GSABenchmark

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:52 -0400

      Commit message:


	  
		
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      Package: SpliceImpactR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:51 -0400

      Commit message:


	  
		
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      Package: SpliceImpactR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:51 -0400

      Commit message:


	  
		
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      Package: hammers

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:50 -0400

      Commit message:


	  
		
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      Package: hammers

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:50 -0400

      Commit message:


	  
		
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      Package: RFGeneRank

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:49 -0400

      Commit message:


	  
		
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      Package: RFGeneRank

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:49 -0400

      Commit message:


	  
		
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      Package: ZarrArray

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:48 -0400

      Commit message:


	  
		
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      Package: ZarrArray

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:48 -0400

      Commit message:


	  
		
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      Package: SpatialArtifacts

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:48 -0400

      Commit message:


	  
		
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      Package: SpatialArtifacts

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:47 -0400

      Commit message:


	  
		
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      Package: jvecfor

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:47 -0400

      Commit message:


	  
		
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      Package: jvecfor

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:47 -0400

      Commit message:


	  
		
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      Package: scPassport

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:46 -0400

      Commit message:


	  
		
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      Package: scPassport

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:46 -0400

      Commit message:


	  
		
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      Package: GenomicCoordinates

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:45 -0400

      Commit message:


	  
		
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      Package: GenomicCoordinates

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:45 -0400

      Commit message:


	  
		
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      Package: MetaboAnnotatoR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:44 -0400

      Commit message:


	  
		
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      Package: MetaboAnnotatoR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:44 -0400

      Commit message:


	  
		
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      Package: SpNeigh

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:43 -0400

      Commit message:


	  
		
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      Package: SpNeigh

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:43 -0400

      Commit message:


	  
		
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      Package: ExpoRiskR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:43 -0400

      Commit message:


	  
		
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      Package: ExpoRiskR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:43 -0400

      Commit message:


	  
		
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      Package: scConform

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:42 -0400

      Commit message:


	  
		
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      Package: scConform

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:42 -0400

      Commit message:


	  
		
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      Package: RNAshapeQC

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:41 -0400

      Commit message:


	  
		
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      Package: RNAshapeQC

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:41 -0400

      Commit message:


	  
		
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      Package: MeLSI

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:40 -0400

      Commit message:


	  
		
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      Package: MeLSI

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:40 -0400

      Commit message:


	  
		
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      Package: sfi

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:39 -0400

      Commit message:


	  
		
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      Package: sfi

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:39 -0400

      Commit message:


	  
		
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      Package: BiocPkgDash

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:39 -0400

      Commit message:


	  
		
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      Package: BiocPkgDash

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:39 -0400

      Commit message:


	  
		
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      Package: fraq

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:38 -0400

      Commit message:


	  
		
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      Package: fraq

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:38 -0400

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      Package: Seqtometry

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:37 -0400

      Commit message:


	  
		
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      Package: Seqtometry

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:37 -0400

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      Package: HiSpaR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:36 -0400

      Commit message:


	  
		
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      Package: HiSpaR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:36 -0400

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      Package: BiocBuildReporter

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:35 -0400

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      Package: BiocBuildReporter

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:35 -0400

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      Package: SMTrackR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:34 -0400

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      Package: SMTrackR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:34 -0400

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      Package: SEMPLR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:34 -0400

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      Package: SEMPLR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:34 -0400

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      Package: MetaProViz

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:33 -0400

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      Package: MetaProViz

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:33 -0400

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      Package: fRagmentomics

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:32 -0400

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      Package: fRagmentomics

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:32 -0400

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      Package: fourSynergy

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:31 -0400

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      Package: fourSynergy

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:31 -0400

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      Package: netZooR

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      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:30 -0400

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      Package: netZooR

      Commit: b26220b66c9754b2cc16294b90106e065cbafbad

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:30 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: GOfan

      Commit: 544d98d706f2d2aedd8f9caaf28a455c9563d762

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:29 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: GOfan

      Commit: 26f6395b6056b364e4695967b99e86ec7e86872c

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:29 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: Battlefield

      Commit: 69a79b679b63d692eca55dcc994d81be2459b113

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:28 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: Battlefield

      Commit: a0574ac55d93df6c279f7eb5da4b815f73c43528

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:28 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: RBedMethyl

      Commit: e60c5b9d2174407312a0cb7ff01b9bac613f5c47

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:27 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: RBedMethyl

      Commit: 08623bb83476847550040301f783c5aa5b6a976a

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:27 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: tidyprint

      Commit: 9177293cacdfea376105d19dd0b4200e3c2dd542

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:26 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: tidyprint

      Commit: 8f2e4814a5feb3ce343e5696b3b0bbb5612e7a7f

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:26 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: toppgene

      Commit: bd58ff06da31fca772b7b665179c8aa1020cb0c0

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:26 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: toppgene

      Commit: 46ffa66b36229c581d8b76f02c0c66ee5ff948c9

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:26 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: OAtools

      Commit: 725e42103a44b8b9abc687cd2886a4baeed57d09

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:25 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: OAtools

      Commit: 1cc067d9f199c2a3a8564bb7b118e88910c5df04

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:25 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: lcmsPlot

      Commit: 84e7f38a8641a076a0f8ff8dc3638db95bb90d8b

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:23 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: lcmsPlot

      Commit: 146cffe811c30b16e27313cb9000d19bfd14ae83

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:23 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: PTMods

      Commit: 08ea1e1bf0c4990872a3c0d2fd2c97276fae7e6d

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:23 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: PTMods

      Commit: 83e201813d38b78c8697538c9f1a0dc13b085af6

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:23 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: Rfastp

      Commit: e419718a583a352c9456d9b7918fdd3a66e639ce

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:22 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: Rfastp

      Commit: a859ea0e5bef2f7bef1a85879ff6e12faff378a1

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:22 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: carnation

      Commit: 4bed175b9a8f21d8ec44da66192989bc893f71de

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:21 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: carnation

      Commit: 2ff883eb4ec105813d70887735930914088a54d3

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:21 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
    

      Package: DenoIST

      Commit: 35bfd0d4b063c8739a6e981edee07bb2932f5948

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:20 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 
    
  
    

      Package: DenoIST

      Commit: 391d87bc67c58cb52539a6cbf60568d841889831

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:06:20 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 
    
  
  


</div>

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