Configure editing setup matrix for dose response curves (#143)

Co-authored-by: Tony Wu <wu.anthon@northeastern.edu> 

 refactor(statmodel): Refactor namespaces for modeling and visualization options (#138)

 

 feature(response-curve): Enable setting up metadata for response curves (#133)

 

 Adding UI/Backend for MSstats+ option for summarizations. (#134)

 

 refactor(statmodel): Finalize namespaces for comparisons components (#131)

 

 feat(spectronaut): Enable calculation of anomaly metrics for Spectronaut Converter (#127)

 

 chore(statmodel,visualizeNetworks): Remove build warnings (#125)

 

 feature(network-interpretation): Add feature to enable user to search for any identifier in subnetwork (#120)

 

 tests(stat-model): Add unit tests to stat model server (#118)

 

 Specify exact = FALSE for testing alternative CI's (#6)
 

 Include rworkflows (#3)

* No separate website for notameStats

* Suggest missForest for vignette
 

 Bumped verion and date, updated NEWS.
 

 Improved detection of non-finite values.

Detection is now handled at the C++ level, either by wrapping the Matrix during
index construction, or by checking each query within the parallel section.

Moreover, the detection check is now optional so users can disable these for
greater speed if they know that no NaNs are present in the input matrix.

Also fixed some doc aliasing for the methods.
 

 fix merging conflict
 

 potential error handling for bfcneedsupdate
 

 Replace @import rols with explicit @importFrom declarations for specific functions

Co-authored-by: shbrief <15724490+shbrief@users.noreply.github.com>
 

 increment version to 1.21.3
 

 resolve Rd warnings, adjust some docs formatting
 

 adjust intercept factor warning (#178)
 

 bump to 1.29.2, cleaned up legacy functions, turn nonuniqMask to backgroundMask
 

 bump to 1.29.1
 

 switching KYCG out
 

 fixed formatting problem in vignette chunk
 

 rename inst/extdata/germline_sequences/ -> inst/extdata/germline_sets/
 

 bump version
 

 reinsert nrows to HDF5DataFrame class
 

 remove old code
 

 Addressed warning messages
 

 Addressed warning messages
 

 added cell_info2
 

  Updated GESS report files.
 

 air and lint
 

 reduced data mannually
 

 updated examples
 

 fix test-visualizeQTL error
 

 Fix Devel-specific errors.
 

 Avoid double dispatch by only calling methods on the prebuilt index.

Renamed all generics to reflect the fact that they operate on the index. All
of the old user-visible functions now just call these underlying generics.

This change allows us to accept non-matrix, non-BiocNeighborIndex inputs,
convert them into a beachmat pointer and pass it to knncolle_tatami so that
we can directly build and query indices from non-ordinary matrices.

Also soft-deprecated BPPARAM= now that we're redesigning the generics.
 

 `dbmanager`: general on-disk RDS cache
 

 `metatlas_gem_tsv`: access to standard GEM auxiliary tables (reactions, genes, metabolites, etc)
 

 `metatlas`: fetch directory trees of standard GEM git repos (`metabolic_atlas_list_gems`); basic functions to access files in git repos
 

 `urls`: general git URLs
 

 `metatlas`: access to standard GEMs
 

 `metatlas`: suppress uncontrolled stdout from `SBMLR`
 

 `metatlas`: removed `dontrun` from docstring example
 

 `archive_extractor`: do not return, but visit `reader` callback also if `to_tempdir` is `TRUE`
 

 `metatlas`: fixed URL for individual models
 

 `metabolic_atlas_model`: download an SBML model from Met. Atlas; first draft
 

 missing headers from R files
 

 Fix: cyGroups follows a different naming structure in the JSON export. Updated the export function accordingly. Also the CyGroup ids have to be present in RCX object, a check for those references has been added.
 

 Fix: cyGroups follows a different naming structure in the JSON export. Updated the export function accordingly. Also the CyGroup ids have to be present in RCX object, a check for those references has been added.
 

 Merge pull request #58 from rformassspectrometry/jomain

Fix for "N/A" reported as retention time and performance improvement 

 ci: use BioC 3.22 on Windows
 

 refactor: performance improvement through data.table::rbindlist
 

 fix: support N/A for rtime
 

 update news
 

 Include CONTRIBUTING.md (#4)

Shows up when making a pull request. 

 new check
 

 load_OrgDb() function was re-exported to ensure compatibility with the clusterProfiler
 

 Robust seqinfo fix and version bump to 1.17.1
 

 Updated markdown to skip examples
 

 Bump version
 

 Enforce chunk and shape being json arrays in v2 metadata

This is more in line with the spec and improves compatibility with other zarr implementations 

 Avoid int -> dbl conversion for unicode nbytes

Fix https://github.com/Huber-group-EMBL/Rarr/issues/81#issuecomment-3757490718
 

 Remove stop() from switch()

For readability
 

 Remove unused var
 

 Run devtools::document()
 

 Add roundtrip test for unicode writing/reading
 

 Simplify and fix unicode writing
 

 Bump version
 

 Allow reading structured datatype
 

 Add parsing of structured data types
 

 Updated warning messages in NewData
 

 update docs
 

 Update package startup message to use yulab_msg 

 fix:auto handle non xenium tx with no qv
 

 bump version
 

 refactor(simplify): restore auto semData calc and add warning

- Restore automatic 'semData' calculation for IC-based methods when 'semData' is missing.

- Add warning message when 'semData' is not provided to inform users about automatic calculation.

- Standardize code by removing pipe usage in 'GO_to_remove' assignment.
 

 temporarily deactivated one unit test with vdiffr (doppelganger)
 

 added new test plot files
 

 updated license notifs date to 2026
 

 bump version
 

 fix(fortify/treeplot/cnetplot): resolve warnings and bugs

- fix(fortify): resolve missing global function/variable warnings in `fortify.compareClusterResult` by importing dplyr functions and using `.data` pronoun
- fix(treeplot): resolve column selection error when color and size variables are identical or named similarly
- fix(cnetplot): align S3 method arguments with generic function and document `categorySizeBy` parameter
- docs: update NEWS.md and regenerate documentation
 

 feat: support categorySizeBy in cnetplot and clean up parameters

- cnetplot.enrichResult: support categorySizeBy passing to ggtangle::cnetplot using do.call to avoid tidy eval issues.

- cnetplot.enrichResult: remove legacy categorySize parameter.

- cnetplot.compareClusterResult: revert changes, removing categorySizeBy parameter.

- Update NEWS.md.

BREAKING CHANGE: categorySize parameter is removed from cnetplot.
 

 fix: goplot error due to GOSemSim update
 

 docs: fix typos and grammar issues in documentation
 

 bug fixed
 

 Merge pull request #340 from qscSeed/devel

fix mismatch between label and data in tableGrob2 

 limpa 1.3.4
- Updates to vignette regarding protein-level input, PTMs and DPU.
- Add toc to vignette.
- Replacing "peptide" with "precursor" terminology in help pages.
 

 Bump version
 

 trying to see if the build check runs
 

 addressed build warnings
 

 Forgot to pass along the method= in clusterGraph.se.
 

 Updated scran_aggregate and added the new factorize library.
 

 make subsetRegion() robust to out of bounds regions
 

 Skip snapshot tests on Bioc
 

 forgot to add coordinate file
 

 updated man pages
 

 Update meta-analysis to follow abundance and prevalence testing in MaAsLin3
 

 update documentation
 

 Updated the README to link to the package vignettes
 

 Resolved some streaming problems
 

 Allowed for multiple FASTQ input files, resolved bug when demultiplexing
empty stringset
 

 Version bump
 

 chore(deps): update pre-commit hook lucas-c/pre-commit-hooks to v1.5.6 (#181)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> 

 version bump in devel
 

 Fix C++ requirement
 

 feat(id-conversion): Support HGNC names as user input (#67)

 

 Merge pull request #23 from systemPipeR/devel

fix varseq add filter and venn steps 

 1. return_feature: replaced rols::Term with rols::olsTerm
2. read_cache: If the cache is older than a certain number of days, the function returns NULL.
 

 Updated issue tempalte
 

 docs update
 

 docs
 

 docs update
 

 -Doc update + bug fix in statistical testing
 

 -Bug Fix and news update
 

 -Bug fix for stats_x
 

 -Fixed Bug regarding new functions accepting all tests in FindMarkers
 

 Minor fixes
 

 - attempt to bump version again to 0.99.7 (due to build issue on Bioc side)
 

 bug fix: my bug fix
 

 Merge pull request #528 from GoekeLab/update_github_actions

update github actions to check push and PR to devel_pre and devel_pre_v4 

 add check of lint for push and PR towards devel_Pre and devel_pre_v4
 

 Merge pull request #525 from GoekeLab/fix_xgboost_parallel_processing_issue

Fix xgboost parallel processing issue 

 fix the bug in unspliced tibble construction. This will fix the dplyr as well.
 

 remove the warning message
 

 Merge pull request #406 from federicomarini/devel

fixing the chunk when showing the import from the TxDb object 

 Merge pull request #520 from GoekeLab/xgboost_x_y_rename

fix xgboost data and label rename to x and y warning 

 resolve the warning caused by using old argument name data and label, and also using verbose argument
 

 fix xgboost data and label rename to x and y warning
 

 update label to logical for testing fixXGboostmodels
 

 update unsupported .model binary format to .ubj for xgboost saved model
 

 re-create terms attributes for lmNDR from formula
 

 fix xgboost label logical issue in junction site prediction step
 

 Merge remote-tracking branch 'upstream/devel' into devel
merge upstream to origin
 

 Merge branch 'Multiplex_Major_Patch' into devel 

 debugging the case when nonuniqueCounts is NULL
 

 Merge pull request #470 from GoekeLab/singleExon_2

remove the lowMemory and update example code for generating rcf 

 fix bug about CompressedCharacterList (revert)
 

 Keep the lowMemory parameter and the warning meaasge
 

 update the example code for generating rcf
 

 remove lowMemory which causes the error when specifying readClass.outputDir
 

 fix rc assignment bug (multi-sample bambu-sc)
 

 Merge pull request #460 from GoekeLab/singleExon_2

Remove the prefix of gtf file 

 remove }
 

 fix bug when cleanReads = T
clipFunction function, undefined argument alignData
 

 fix bug about CompressedCharacterList
 

 fix importBambuResult when prefixes = ""
remove some rudanduant rows in writeCountsOutput functions
 

 fix prefixes pass
 

 fix writeBambuOutpur error when this is no novel transcript in se object
 

 improve flexibility for BC&UMI parsing
 

 remove prefix "extended_annotations"
 

 Merge pull request #458 from GoekeLab/Multiplex_Major_Patch

Merge Multiplex to singleExon_2 

 update function documentation
 

 fix bug for reading in spatial files
 

 update code style
 

 update documentation
 

 allow reads be NULL when quantData is provided for quant mode only
 

 fix bug for demultiplexed when demultiplexed is provided as a file
 

 comment unused code after return in generateUniqueCounts function
 

 add documentation for barcodesToFilter argument and update the formats for some paragraphs
 

 fix barcodesToFilter not working bug
 

 min.txScore.singleExon bug fix
 

 bug fix for 0 value quantification
 

 Fix bugs due to fusion mode on test data

 

 Add lowMemory replacements to documentation and importBambuResults

 

 return distTable now returns intermediate distTable

 

 max recommended NDR is now 0.999

 

 Fix formatting in docu

 

 Clean up cluster discovery

 

 Add in descriptions for new arguments

 

 Return default degbias to on

 

 Fix quantification when running bulk

 

 Fix mode

 

 Add in preset modes

 

 Update remaining test data

 

 Update xgboost models and include code to redo it

 

 Add the flags in writeBambuOutput to control which gtfs are written

 

 Restore seperateSamples argument in writeBambuOutput lost in merge

 

 update actions versions
 

 Fix merge

Combine the change to unspliced read mutating with the inclusion of sample id
Fix bug during extendAnno where wrong variable was provided when determining the number of novel genes
 

 Update release history

 

 Merge branch 'remov_SE_combineAnno' into Multiplex_Major_Patch

 

 Dont filter out reads that align up to the last nucleotide - fusions

 

 catch error when 0 or 1 genes have counts


same error

 

 undo EM counts naming

 

 bug fix missing sampleNames

 

 Track sample names into quantData

 

 Make sure column names are present when providing clusters

 

 tidy up

 

 Update low memory to process read classes together or seperately

This makes lowmemory readclassconstruction base line 

 AssignDist step will now output uniqueCounts

transcriptToGene will work on this se object 

 Enable clusters to be assigned before EM


tidy up


typo


fix

 

 return non em counts before quant step


fix use of placeholder variable name

 

 fix bug when reading in barcode map from file

 

 clean up warnings

 

 importBambuOutput function

 

 Fix flexible barcode lengths

 

 read in attributes as rowData

 

 Seperate umi dedup from cleanReads

 

 Flexible BC and UMI lengths

Also will warn if UMIs arn't provided and if there are reads without barcodes 

 keep txScore in extendAnno

 

 Transcript discovery at cluster level

 

 add extra messages

 

 Merge branch 'devel' into remov_SE_combineAnno 

 Tidy up clean reads

 

 Enable messyForest to take in multiple samples

can use the sampleName parameter to decide if the barcodes of two different files should be combined or treated as seperate. I.e if you have a technical replicate you would give them the same samplename where as a biological replicate would have different sample names 

 Remove warning about bambu annotations if discovery not being done

 

 added ifelse test for spatial
 

 updated gzfile function
 

 update quantification output file format
 

 fixing the chunk when showing the import from the TxDb object
 

 reallow deg bias

 

 Resolve lack of incompatible rcs better

 

 Enable Bambu to restart with readClassDt to help with R hogging memory

 

 Stop incompatibleCounts from being converted away from sparseMatrix

 

 Add in helper splitReadClassByRC for old functionality

 

 Tidy up

 

 Fix bug where counts were not assigned to correct transcripts

Now disttable and splitting of read class counts is done in the quant step 

 Speed up addAval

 

 add in missing variable

 

 Clean up distTable code

 

 Reduce memory input to threads

 

 Remove progress bar

 

 fix bugs

 

 Enable demultiplexing and speed up splitReadClassFiles()

 

 bug fix the merge

 

 MessyForest

 

 Also tidy up

 

 Clean up bambu.quantify and add calculateEqClassCounts

 

 Move getUniCountPerEquiRC outside bplapply

 

 quick fix hack to enable readGrgList as input

 

 Ensure eqClasses is recalculated when setting NDR

 

 Fix bug when rcOutDir not used

 

 Fix typo

 

 Update documentation with writeAnnotationsToGTF

 

 4th GTF of novel transcripts only

 

 fix setNDR test

 

 Unit tests for reading and writing NDR and txScore

 

 Fix includeRef bug 

 

 Assign names to transcripts earler so subset and lowConf are given names

 

 Add documentation to setNDR and carry arguments over

 

 NA's are loaded in as NAs from GTF

 

 Add txScore to mcols 

 

 Allow setNDR to work on gtf files that are read in

 

 write NDR to gtf

 

 readClass warnings kept only when rcFile is made and not when loaded in

 

 Revert "Add helper function to set NDR on extendedAnnotations"

This reverts commit 9b865dfa334e22774a9e51fd829afd23b7e27181.
 

 Add helper function to set NDR on extendedAnnotations

 

 Add lowConfidenceTranscripts to metadata and speed up relSubsetCount

 

 Remove SE from being combined during extendAnno

 

 fix: refactor cache initialization and reading for robustness
 

 ignore file
 

 use cache mechanisms from yulab.utils; enhance godata validation; refactor internal checks
 

 Import the metabolite data from csv file
 

 Update
 

 Address deprecation warning in frollapply
 

 fix namespace file
 

 Various changes:

- Add germline V gene annotation file to AIRR builtin germline dbs
  for human and rhesus monkey.

- Add 'check.data' argument to write_V_ndm_data().

- Add parallel computing examples to man page for igblastn().
 

 add s3_client check to read_zarr_attributes (#99)

* add s3_client check to read_zarr_attributes

* lint package

* change default of s3_client

* fix documentation

* Use snapshot test for reading attrs on s3

* Mention read_zarr_attributes() s3 change in NEWS

* Bump version

---------

Co-authored-by: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>