Update getGeneSets.Rd
 

 Merge branch 'main' of https://github.com/dozmorovlab/scHiCcompare
 

 Merge pull request #13 from dozmorovlab/devel

Merge pull request #12 from dozmorovlab/main 

 update mice functions
 

 Merge pull request #12 from dozmorovlab/main

merge 

 Merge pull request #11 from dozmorovlab/devel

Devel 

 Merge pull request #10 from dozmorovlab/devel

update package 

 Bump version 0.99.35, fix data usage docs
 

 Add @usage documentation for data objects
 

 minor test
 

 Add link to https://youtu.be/bzzPBt3Mz0A and the LIBD RStats notes
 

 Merge pull request #5 from sgunz/msmc_analysis

# sosta 0.99.5

* New Analysis Functions: Added `assignCellsToStructures`, `calculateBorderMetrics`, `calculateCellTypeFractions`, `calculateDistanceToBorder`, `calculateDistanceToTissueRegion`, and `calculateTissueRegionFractions` to improve spatial and structural analysis.  
* Simulated data set: Introduced a new data set for testing and demonstrating package capabilities.  
* Vignette update: Expanded documentation to include multi-sample and condition-based analysis.  
* Bug fixes & optimizations: Addressed various issues and improved performance.  
* Code cleanup: Enhanced readability, maintainability, and structure. Consistent use of camelCase for function arguments.
 

 changed to ggplot, styling
 

 more edits
 

 some edits / code suggestions
 

 bump version
 

 vignette updated
 

 vignette renamed
 

 added border metrics
 

 vignette with sim data
 

 examples adapted
 

 added new function assingCellsToStructures
 

 v0.99.35 -- added a LICENSE.md file as requested by the journal
 

 Meet Bioconductor requirements
 

 fix: correctly consider ties in reduce()
 

 Remove one line calling Rgraphviz functions to see whether the core dump in the build system for nebbiolo1 dissappears
 

 change pmid prefix from PMID to pubmed in doc; optimize error notification in pgxSegprocess
 

 Merge pull request #8 from rformassspectrometry/jomain

Add function to delete locally cached files and avoid wiping cache in unit tests 

 ci: install netcdf on macOS
 

 version bump
 

 update vignette
 

 bug fixed intersection
 

 Merge branch 'RELEASE_3_20' of https://github.com/lisiarend/PRONE into RELEASE_3_20
 

 Merge branch 'main' into RELEASE_3_20 

 enrichment updated
 

 citation added
 

 Merge branch 'RELEASE_3_21' into main 

 fix enrichment bug
 

 update news
 

 Updated the readme and vignette content to ensure the information is detailed and accurate.
 

 Updated the spread and clustering parameter default values.
 

 Updated the default value of some clustering parameters. Modified the column names for clusters and subclusters generated from first clustering step.
 

 Moved all the helper functions to utilities.R script.
 

 update news and restrict BH version
 

 sprintf was replaced with snprintf to remove WARNINGs.
 

 v1.0.0: Update version number to signify stable release
 

 v1.9.11 -- Merged #102 that fixes a bug in `vis_clus()` for coloring NA values
 

 Don't treat NA as a color (separate from 'na_color' in vis_clus), leading to expected behavior when there are 12 clusters with some NAs and colors and provided by the user
 

 updating the version
 

 Merge pull request #269 from amcdavid/docupdate

Freshen docs 

 Merge pull request #268 from amcdavid/oz-ports

Changeset from //packages/

formatting and doc updates
.gate_custom
removes cytokine gate
Bugfix to preprocessing with empty popAlias
extracts Cdqrls from stats package, adds lm_wfit_cpp 

 update cpp11 i guess
 

 update rlm tests
 

 keep gate_mindensity here
 

 ODC177 add error for empty gatingTemplates in constructor.
 

 selected changes from //packages/openCyto
 

 add new from //packages
 

 v.1.9.10 -- mention updates implemented on #101 by @lahuuki
 

 Update a bit the `gene_name` argument info: small formatting changes.
 

 Add test for sig_genes_extract() - test flexible gene_name
 

 Add gene_name variable
 

 scDotPlot v1.1.1
 

 fixed length(k2)==0
 

 Merge pull request #382 from Caris-Life-Sciences/fix-bai-option-coverage-r-272

use --bai option value when a single bam file is provided as input 

 chore: bump patch version
 

 update EHub IDs for vignette examples
 

 doc: update documentation to use \code{} for XevaSet object reference
 

 add unit tests
 

 sanitize parameter description
 

 sanitize parameter description
 

 fix accessing element
 

 Merge branch 'devel' of github.com:plger/scDblFinder into devel
 

 added an output type
 

 added mention of older wrong dbr.per1k in vignette
 

 updated pkgdown workflow
 

 fix error due to empty indice vector
 

 Updated users guide for the next major release.
 

 Update author information for package
 

 Minor improvement of doc format
 

 version bump 1.33.4
 

 minor edit
 

 Merge branch 'master' into devel

fixes for 3.21 release
 

 Update clonalCompare.R
 

 Update test-coverage.yaml 

 update
 

 temp fix for BRISC_estimation R 4.5
 

 Bump to 0.99.5. Why is the package looking for 'scuttle'?
 

 Changed to Western email address.
 

 Merge pull request #100 from gdrplatform/GDR-2893

Gdr 2893 

 refactor: appease lintr
 

 refactor: update as per review
 

 refactor: update logic for meta data
 

 refactor: add support for OncotreeLineage in PRISM data
 

 1.8.1
 

 stash
 

 chore: fix tests
 

 chore: update tests
 

 many changes to avoid readr::read_tsv and deal with bad records in new gwascat payloads from EBI
 

 Width/height options for plotAbundanceDensity (#179)

 

 add DSP
 

 Update README.md 

 Bump version
 

 merge changes to spatCor() documentation from devel and from #231
 

 modify spatCor() to use .check_assayNames() similar to parameter object constructors
 

 implemented and documented according to #231
 

 Bump version
 

 basilisk.R
 

 .

Merge branch 'devel'

# Conflicts:
#	DESCRIPTION
#	R/xCell2Train.R
 

 .
 

 Update README.md

remove badges 

 Update README.md

add badges 

 modifying message language re #111
 

 Merge pull request #46 from microbiome/prevalence

Prevalence 

 Minor changes
 

 Fix RDA example and initialise PrevalencePlot
 

 Fix utils vignettes
 

 Add citation
 

 Reorganise utils
 

 v1.3.3
 

 Fixed a bug that prevented the use of local miRTarBase copies.
 

 Merge pull request #49 from LTLA/venv

Switch to virtual environments with a native Python install (via reticulate+pyenv).  Passes check on VJC mac 

 Allow users to override the Python binary.
 

 Cleaned up links in the docs to pass Check.
 

 Completed the strip of conda-related information.
 

 Combine some functions from basilisk.utils.
 

 Try out the migration to virtualenvs.
 

 Merge pull request #152 from gdrplatform/GDR-2909

Gdr 2909 

 refactor: appease lintr
 

 refactor: update as per review
 

 refactor: update as per review
 

 doc: reoxygenate
 

 refactor: move fun
 

 Fix a typo on the NEWS info
 

 Mention how to deal with an OS breaking and if you want to ignore it.
 

 Test release 3.19
 

 Test new case that will enable users to specify bioc-release, bioc-devel, or name a specific version number like "3.20"
 

 Update the template file since setting the CRAN repo to use package manager does work for Linux.
 

 Try using the CRAN RStudio package manager on Linux
 

 Don't need to set the upload-artifact name using hardcoded names anymore
 

 I don't think that we need to set the ENV CRAN variable anymore
 

 Make the option name more self explanatory. Add a comment clarifying how this will be used.
 

 Try fixing JSON syntax
 

 Fix name
 

 Be a bit more verbose, fix bioccont for latest_release = 'true'
 

 Play around a bit with setting the config matrix on a previous job
 

 Add a link to https://packagemanager.posit.co/client/#/repos/bioconductor/setup
 

 Might not need to specify RSPM anymore. Let's check
 

 1.9.0
 

 Err, forgot to save this file prior to the last commit
 

 Try setting R_LIBS_USER on Linuxa and saving it to the GitHub environment
 

 Sync the two check-bioc.yml files
 

 Thanks to https://github.com/r-lib/actions/commit/04b9574af4412e3dc229e5e17dbbfe7cdac8dd3b from https://github.com/r-lib/actions/issues/912#issuecomment-2667950006, the conditional code for R home might no longer be needed. Let's test this.
 

 Test cache. Also fix a NOTE on utils::browseURL() at https://github.com/lcolladotor/biocthis/actions/runs/13933418862/job/38995897728#step:20:88
 

 empty renv test
 

 GitHub actions didn't like this comment on the yml file:

https://github.com/actions/cache/blob/d4323d4df104b026a6aa633fdb11d772146be0bf/examples.md?plain=1#L566-L592
 

 Bump v0.99.34, document & style
 

 Style package, bioc_style()
 

 Follow the current guidelines from https://contributions.bioconductor.org/description.html#description-bugreport
 

 SparseArray 1.7.7

Make rowsum() and colsum() work on any dsparseMatrix derivative and not
just on a dgCMatrix object. For example now they also accept a dgRMatrix
or dgTMatrix object.
 

 enrichment analysis updated
 

 Remove some vignette template lines as noted in https://github.com/Bioconductor/Contributions/issues/3503#issuecomment-2551233199
 

 v1.17.2 -- update some things to more closely match what was required by Bioconductor at https://github.com/Bioconductor/Contributions/issues/3503#issuecomment-2551233199.
 

 Auto-code formatting with Air
 

 Auto-style with Air
 

 Link to https://contributions.bioconductor.org/general.html?q=unnec#undesirable-files and https://github.com/Bioconductor/Contributions/issues/3503 on the docs explaining why `dev/` is not version controlled.
 

 updated version numbering
 

 Merge branch 'devel' of https://github.com/jessmcc22/BatchQC into devel
 

 Merge pull request #107 from jessmcc22/devel

Restored sva correction method; Added umap 

 Merge branch 'devel' of https://github.com/jessmcc22/BatchQC into devel
 

 Added an exploratory option to umap function that plots a grid of different minimum distances and k nearest neighbors
 

 Updated Version number
 

 Added umap function
 

 Merge pull request #106 from jessmcc22/devel

Added Ellipses to PCA; Set Max value to max of data set; corrected BicCheck errors 

 Added ellipses to PCA plot and set default features to plot to the max of the data set
 

 Set p-value scale to always be 0 to 1 in differential expression analysis
 

 Merge branch 'devel' of https://github.com/jessmcc22/BatchQC into devel
 

 Merge pull request #105 from jessmcc22/devel

Added limma 

 Added limma as a correction method
 

 Updated version number
 

 Merge pull request #103 from jessmcc22/devel

Updated DESeq2 binomial check to include pval information 

 Added pval info to DESeq2 binomial evaluation
 

 v2.2.4

overhaul of getGeneSets due to msigdbr change
 

 v1.17.1 -- update to use actions/cache@v4 instead of v3
 

 Removed installation of cmdstanr on load
 

 specify what is meant by 'consistency' of IDs
 

 feat: automatically infer `symmetrical = FALSE` and limits when plotting only trans contacts
 

 feat: in multi2Dquery of only trans interactions, manually return balanced instead of expected/detrended
 

 fix: support chromosome names containing "_" or "-"
 

 bump to 1.7.1
 

 doc: add CITATION
 

 bump version
 

 add chopBy param, update test to make it fail
 

 fix tests based on review & bump version
 

 debug: update docs
 

 :wq
bump version
 

 mimic the usual call, cover full=TRUE
 

 rm obsolete code
 

 fix broken bioconductor vignette link 

 Update plotting.R
 

 Version bump
 

 Setting "report=FALSE" in all relevant files

Merge remote-tracking branch 'origin/master' into devel
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
 

 Simply setting report = FALSE in examples

Also removed tempdir() as it is no longer needed.
 

 Merge pull request #7 from rformassspectrometry/repeat_download

refactor: add code to retry download 

 ci: update cache version
 

 ci: use R devel for all platforms
 

 bump up to current bioc version
 

 Merge pull request #111 from ImmuneAxisa/vanilla_grp_mutate

Speed up group mutate operations 

 try v4 for actions
 

 vanilla group mutate for mcols
 

 update maintainer email
 

 Correct spelling mistakes
 

 Bug fix in calling getFixedParameter() in .getParams()
 

 Update manuals
 

 pull from Bioc

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

# Conflicts:
#	DESCRIPTION
 

 Merge pull request #324 from stemangiola/resolve-confounders-without-altering-original-columns

Resolve confounders without altering original columns 

 update function and documentation
 

 Merge branch 'adapt-to-h5' of https://github.com/stemangiola/tidybulk into adapt-to-h5
 

 fix docs
 

 fix gene enrichment internal arguments
 

 make the test less strinct
 

 update docs
 

 take care of matrix conversion
 

 Merge pull request #318 from stemangiola/update_confounders_and_filtering

Update confounders and filtering 

 add design to filtering
 

 Merge branch 'master' of github.com:stemangiola/tidybulk
 

 version UP
 

 updates and unittests for msigdbr >= 10.0
 

 adds tests for updated msigdbr.

The new msigdbr refactoring hasn't been fully completed, but this works for now with the (a) new msigdbdf backend.
 

 ensure genesets are not reordered when retrieving ora results
 

 adds taxonomy ids to species_info outputs
 

 Merge branch 'master' of github.com:FertigLab/dominoSignal
 

 Merge pull request #150 from FertigLab/149-circos-plot-ligands-in-rl_map-but-not-expression

149 circos plot ligands in rl map but not expression 

 expected messages as character vector
 

 obtain_circos_expression checks for ligands in signaling matrix

If only some of the ligands are present, a message is sent explaing which ligands will be plotted. If no ligands are present, an error message is returned.
 

 error message for no ligand circos plot test
 

 increment version 1.0.4
 

 add Dockerfile, add container action, close #146
 

 test case for plotting with cell types including hyphen
 

 ligand chord colors by name instead of index
 

 cell_idents removed as argument to render_circos

All selection and subsetting of cell types to be plotted will occur in the obtain_circos_expression function. render_circos_ligand_receptor will always plot everything in its signaling_df argument
 

 initial circos tests

tests:
- does the parent circos function containing the two modular functions render a plot without error
- when a single ligand is specified, is the plotting data frame correctly subset
- if no ligand is specified, an error is returned
 

 Merge branch 'circos_factorization' of https://github.com/FertigLab/dominoSignal into circos_factorization
 

 Update documentation
 

 example receptor argument
 

 specify circos sender cell_idents
 

 Merge branch 'dev' into circos_factorization
 

 Merge pull request #145 from FertigLab/dev

Functions to average gene expression by clusters and for complexes 

 v1.0.2 documentation and logging
 

 Files required for pkgdown customization
 

 use single receptor as argument to render_circos
 

 Merge branch 'circos_factorization' of https://github.com/FertigLab/dominoSignal into circos_factorization