limma 3.63.10

- Update limma-Tests.Rout.save for R 4.5.0.
 

 refactor: add exmaples
 

 refactor: update unit tests
 

 chore: resolve conflict
 

 chore: bump version and update NEWS.md
 

 test: move tests
 

 Test using the biocthis v1.17.4's use_bioc_github_action()
 

 v1.17.4 -- announce the major changes to `use_bioc_github_action()`
 

 Update use_bioc_github_action() and test it.
 

 Fix else if linux syntax
 

 Hm... XML fails to install on macOS with bioc-release using RStudio's package manager
 

 Test on release after wiping out the caches on GitHub Actions
 

 Test with bioc-devel using CRAN = "https://packagemanager.posit.co/cran/latest"
 

 Make it such that r-lib/actions@setup-r recognizes that R version to use
 

 Test with bioc-devel
 

 Add soem comments
 

 Forgot to include >> "$GITHUB_OUTPUT"
 

 Fixed echo bash syntax by testing on a Linux server
 

 Try to fix spacing on the yaml file
 

 fix warning
 

 Fix syntax
 

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

 v1.17.3 -- made updates to the GitHub Actions workflow to simplify the code for caching R packages. This reduced some code duplication that existed across macOS/winOS and Linux.

Related to https://github.com/r-lib/actions/issues/912. Also related to https://github.com/r-lib/remotes/commit/0e4e23051041d9f1b15a5ab796defec31af6190d in terms of being able to support Linux system dependencies on Ubuntu 24.04 in the near future.
 

 Sync the check-bioc.yml files again
 

 See if creating R_LIBS_USER works on Linux
 

 Make changes in preparation for https://github.com/r-lib/remotes/commit/0e4e23051041d9f1b15a5ab796defec31af6190d being released to CRAN. Aka, they are about to add support for ubuntu 24.04 in remotes such that remotes::system_requirements("ubuntu", "24.04") will work. Currently the Bioconductor docker image is running on Ubuntu 24.04, hence why this will be important.
 

 Update template file after recent cache v4 tests
 

 Move away from https://github.com/actions/cache/blob/main/examples.md#r---renv
 

 Hm....
 

 use BiocFile(List)
 

 Add note on RNAScope details
based on correspondence w/ Penghui Huang
 

 Update to use renv for caching packages. Adapted the code from https://github.com/actions/cache/blob/main/examples.md#r---renv. Specifically from https://github.com/actions/cache/blob/d4323d4df104b026a6aa633fdb11d772146be0bf/examples.md?plain=1#L566-L592
 

 Updated README files
 

 Link also to https://github.com/Bioconductor/Contributions/issues/3501#issuecomment-2408081535
 

 Beef up the news for v1.17.2
 

 I disagree with this request at https://github.com/Bioconductor/Contributions/issues/3503#issuecomment-2551233199 to no longer have a vignettes/.gitignore file. However, well, the vignettes/*.html and vignettes/*.R files can be ignored on the main .gitignore, so I've moved this code there. The overall goal is to help prevent new R package developers from version controling these files that they might generate if they locally render the vignettes.
 

 don't need fs::path() here
 

 Update the default value of use_bioc_description(report_bioc) from TRUE to FALSE to match the current recommendations at https://contributions.bioconductor.org/description.html#description-bugreport that were also mentioned at https://github.com/Bioconductor/Contributions/issues/3503#issuecomment-2551233199.
 

 Remove dev files with: git rm --cached -r dev; echo 'dev' >> .gitignore
 

 Ignore the dev directory on Git. Matches expectations listed by Bioconductor at https://github.com/Bioconductor/Contributions/issues/3503
 

 Merge pull request #108 from jessmcc22/devel

Updated versioning to properly reflect devel 

 update version numbering to match devel
 

 Added sva variation correction method
 

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

 updated variation ratio to be a log
 

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

 Added umap function
 

 Created smaller functions in the nb check for DESeq
 

 Updated email address
 

 Updated Variation ratio explanation to be correct
 

 Updated Violin plots to actually plot the violin portion
 

 removed set_seed() from DESeq2 negative binomial check
 

 Merge pull request #104 from jessmcc22/devel

Updated SE import to not require an assay named "counts" 

 Updated SE object import to no longer require that one assay be called "counts"
 

 Updated version and news
 

 Merge branch 'master' into devel
 

 Update Links
 

 Bumped version
 

 Fixing issues raised by checking with --as-cran
 

 bump to 1.9.1
 

 bump to 1.7.1
 

 ci: fix GHA
 

 ci: update docker names
 

 ci: update branch/docker names
 

 Merge pull request #45 from genesofeve/44-result-format-in-sparse-implementation-when-fulltrue

44 result format in sparse implementation when fulltrue 

 fix the output, close #44
 

 Merge pull request #42 from genesofeve/39-errors-in-projectr-method-for-sparse-matrix-data

39 errors in projectr method for sparse matrix data 

 geneMatchR() could not handle big data - revert it
 

 Merge branch 'master' into 39-errors-in-projectr-method-for-sparse-matrix-data
 

 fix no definition for class “LinearEmbeddingMatrix” warning
 

 works with dgCMatrix now
 

 Merge pull request #41 from KaiAragaki/patch-1

fix broken bioconductor vignette link 

 Merge pull request #40 from genesofeve/projectionDriveR

Projection drive r 

 Plotting updates

Fixed small bug where plots would not display due to cowplot::get_legend() returning many components. Resolved ggplot2 warnings printed to console due to use of `stats$label` rather than `label`
 

 Replace

  array(unlist(m, m), c(dim(m), 2))

with

  array(c(m, m), c(dim(m), 2))
 

 Merge pull request #8 from MetaboComp/fix-file-saving-in-examples

Simply setting report = FALSE in examples 

 update plotHeatmap function
 

 refactor: add code to retry download
 

 docs: update editorconfig
 

 tests: complete unit test coverage
 

 version bump
 

 Merge branch 'tidyomics:devel' into vanilla_grp_mutate
 

 version bump
 

 Merge branch 'tidyomics:devel' into master
 

 update imports and Namespace
 

 version bump
 

 Error on both formula and named effects
 

 fixed logic for sorting exons for junction reporting.
 

 Merge pull request #325 from stemangiola/comply-with-breaking-changes-for-msigdbr

fix docs 

 update docs
 

 Merge pull request #321 from stemangiola/adapt-to-h5

take care of matrix conversion 

 take care of matrix conversion
 

 Merge pull request #323 from stemangiola/comply-with-breaking-changes-for-msigdbr

fix gene enrichment internal arguments 

 Merge pull request #322 from stemangiola/comply-with-breaking-changes-for-msigdbr

Enhance entrez_over_to_gsea function by adding msigdbr version check,… 

 Enhance entrez_over_to_gsea function by adding msigdbr version check, improving data processing, and updating gene collection filtering. Adjusted test for gene over-representation to reflect new expected p-value.
 

 Enhance documentation for UMAP functions and improve parameter descriptions in identify_abundant and keep_abundant methods
 

 version UP 

 Merge pull request #319 from stemangiola/drop_env_for_enquo

use a function to drop env 

 use a function to drop env
 

 improve man
 

 accept df
 

 fixes GO prefixs in getMSigGeneSetDb for GO subcollections in mouse
 

 Support new msidgbr package/dataset split
 

 Fixes issue where fgsea::fgseaMultilevel returns pathways in slightly different order
 

 update to dev numbering
 

 Merge pull request #151 from FertigLab/dev

update to version 1.0.5 

 update documentation v1.0.5
 

 circos ligands unit tests

Tests add two ligands to one of the receptors in the test data. Tests that messages are returned for receptors where only one of three ligands is in the singaling matrix. If all the ligands are absent, checks that an error is returned.
 

 Merge pull request #136 from FertigLab/circos_factorization

Circos factorization & Regex fixes for cluster names 

 remove comments for old circos tests
 

 Merge pull request #148 from FertigLab/146-create-docker-container-on-push-to-main

add Dockerfile, add container action, close #146 

 temp_dir graphics device in testing
 

 alphabetical order of cell_colors palette

Ensures that the order and naming of colors in the legend rendered alongside the circos plot syncs with the alphabetical order of cell types in the circos plot
 

 cell_ident subset in obtain_circos_expression
 

 Merge pull request #147 from FertigLab/dev

increment version number v1.0.3 

 ignore vignette test render dirs
 

 Update render_circos_ligand_receptor.Rd
 

 cell_colors circos argument documentation
 

 arc_name grouping

uses gsub restricted to the end of the arc names of "-[ligand]" to avoid issues where cell types with hyphens in their name could not be plotted
 

 lapply basis for circos expression function
 

 increment version number v1.0.3
 

 Functions to average gene expression by clusters and for complexes
 

 Merge pull request #144 from FertigLab/krishnan_pkgdown_update

Files required for pkgdown customization 

 Update documentation
 

 specify receptor name within render function
 

 update documentation
 

 remove hyperlink in obtain_circos documentation

The brackets seem to be preventing being able to run the lines defining the function following the roxygen comments.
 

 Merge pull request #141 from FertigLab/dev

Functions to map complex names and ligand names to gene names. Restored GitHub actions 

 Merge pull request #143 from FertigLab/actions_restore

restore github/workflows from 0.99.4 

 Merge pull request #142 from FertigLab/krishnan_53_null

Check for list of only NULLs in signaling from complexes 

 When list of complexes only contains NULL values, it will not be added to the existing signaling information.
 

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

 complete roxygen documentation
 

 remove group argument
 

 replace regex calling of sector names with startsWith

Used to avoid errors in pulling parts of sector names due to regex characters appearing in someone's cell type names.
 

 fix indents highlight.sector
 

 append ligand and receptor columns to signaling_df
 

 parse ligands within the render function
 

 render takes a solo signaling_df
 

 initial division of wrangling and plotting
 

 Merge branch 'v0.2.2_development'
 

 fixing findGenesOfInterest to avoid NAs in SpaceMarkers output. (#64)

* fixing findGenesOfInterest to avoid NAs in SpaceMarkers output.

* added comment

---------

Co-authored-by: adeshpa6 <adeshpa6@EB-ONC-G73GXG9.local> 

 updating test and removing notes
 

 rectified the logic for qvalue calculation
 

 bump version
 

 return empty list if no genes pass fdr threshold
 

 Update main.nf 

 add sample id to plot subtitle
 

 debug examples
 

 add interacting gene plots
 

 factors for overlapScores
 

 Merge branch 'main' into nextflow
 

 Update main.nf

fix a bad typo 

 Merge pull request #59 from DeshpandeLab/58-add-hotspot-computation-before-calling-getpairwiseinteractinggenes-in-nextflow-mainnf

58 add hotspot computation before calling getpairwiseinteractinggenes in nextflow mainnf 

 address review comments in pull 59
 

 debug tests
 

 update docs
 

 Update DESCRIPTION 

 Merge pull request #57 from DeshpandeLab/atul-additions

Atul additions 

 Minor typo fix
 

 Merge remote-tracking branch 'origin/main' into atul-additions
 

 Remove extra files
 

 avoid overwriting mqc report (#56)

 

 52 update publish dir (#54)

* use features name as prefix

* debug dir create

* propgatate subdir further

* debug subdir var assignment 

 Hotspots:
 

 49 spacemarkers nextflow module (#50)

* init add nextflow module

* replace to nextflow dir for clarity 

 Delete man/getSpatialParametersExternal.Rd 

 Deprecated getSpatialParameters. Updated tests to be compatible with resolution scaling as specified in getSpatialParamsExternal.
 

 Merge pull request #44 from DeshpandeLab/43-push-current-version-to-bioconductor

43 push current version to bioconductor 

 fix lazyloading issues
 

 chore: update json settings
 

 Merge branch 'main' into GDR-2876
 

 feat: improve logic in `get_assay_req_uniq_cols`
 

 No idea why there are some diffs in this file. oh well :shrug:
 

 syntax typo :face_with_head_bandage:
 

 doc changes
 

 meant to use 'sym()'
 

 styling changes and verbose erroring for plyxp, instead of reporting '.f()', it will report the named function, if possible
 

 making report of an error more verbose if it were to happen within the dots or particular group
 

 reducing redundant code
 

 This should now work on pillar 1.10.0 and earlier
 

 adjusting readme language
 

 technically the start of the bioc:devel branch
 

 plyxp_on, is a neat short hand function
 

 Merge pull request #140 from FertigLab/95-default-number-of-patterns

95 default number of patterns 

 update examples, debug params
 

 update vignette
 

 add a test that fails if no natterns specified
 

 Merge branch 'master' into 85-cpp-tests 

 Manually install fgsea 

 Merge pull request #137 from FertigLab/nextflow

add anndata to dgcmatrix conversion 

 Merge pull request #136 from FertigLab/nextflow

debug adata to dgc mat 

 Merge pull request #135 from FertigLab/nextflow

add anndata to dgcmatrix module 

 Merge pull request #133 from FertigLab/filtered-bc-mat

filtered instead of raw 

 Merge pull request #131 from FertigLab/123-test-behavior-with-a-matrix-fixed

bump version 

 Merge pull request #130 from FertigLab/126-nextflow-module

add reporting 10x by default 

 Merge pull request #129 from FertigLab/126-nextflow-module

parametrize module 

 Merge pull request #128 from FertigLab/126-nextflow-module

126 nextflow module 

 Merge remote-tracking branch 'origin/master' into 126-nextflow-module
 

 0 instead of NULL to avoid warning
 

 disable meanChisq when fixed as Amean/Pmean are 0s
 

 make fix matrix tests faster
 

 Merge branch '123-test-behavior-with-a-matrix-fixed' of github.com:FertigLab/CoGAPS into 123-test-behavior-with-a-matrix-fixed
 

 init: copy module from co-space
 

 update from bioc, bump version
 

 Merge remote-tracking branch 'upstream/devel' into 123-test-behavior-with-a-matrix-fixed
 

 put the comments back
 

 update fixed matrix test to accept all 0s
 

 fix error: comparison between pointer and integer
 

 add second file fixed by mfo@jh.edu
 

 Revert "Merge branch '123-test-behavior-with-a-matrix-fixed' of github.com:FertigLab/CoGAPS into 123-test-behavior-with-a-matrix-fixed"

This reverts commit ab6236971bc6c680e599f75287e607995fc8813d, reversing
changes made to a837c6ba7246f8b83bd0db357f9830c6439ca5eb.
 

 Merge branch '123-test-behavior-with-a-matrix-fixed' of github.com:FertigLab/CoGAPS into 123-test-behavior-with-a-matrix-fixed
 

 add fix received from mfo@jh.edu by email
 

 add fix received from mfo@jh.edu by email
 

 test that the fixed A is returned in result
 

 add a test for fixed P
 

 bump x.y.z version to odd y following creation of RELEASE_3_20 branch
 

 adding comments
 

 expanding comments in GapsRunner.h
 

 Update build-push-container.yml 

 Merge pull request #121 from FertigLab/119-build-container-on-merge-to-main

119 build container on merge to main 

 fix biocmanager package installation
 

 add dockerfile
 

 Merge pull request #120 from FertigLab/119-build-container-on-merge-to-main

add container build action 

 add container build action
 

 Merge pull request #118 from FertigLab/116-wrong-chisq-reported

116 wrong chisq reported 

 ran autoconf, so configure now is with 2 tests from cpp_tests
 

 Revert "another take on bringing the reported/calculated closer together"

This reverts commit 3b669d0f7795a8ead4917e54f09d653ad02f6515.
 

 Revert "unconditionally run cpp tests"

This reverts commit ebea007fb057cea185457bb3e1dd16f2512bceba.
 

 Revert "shrink ch^2 diff with direct calc to 4426 - 4426 == -0.000145"

This reverts commit 5fea9f88ad2fce7b52a488ddb047e7115fa04889.
 

 change tolerance for chisq diff to float precision * n elements
 

 update cpp test doc
 

 commented nonworking test
 

 we added the sparce vector test to what we can run
 

 tag \[vector\] added to vector test
 

 added REQUIRE
 

 update testthat linkingg
 

 init Sasha's approach to tests
 

 add a dummy test w/unc vs wo/unc
 

 add a test that fails (probably wrrong)
 

 a merge for bioconductor
 

 update score description
 

 update docs
 

 refactor patternMarkers - make modular
 

 Merge pull request #110 from FertigLab/109-fix-threshold=cut-mode

add threshold = "cut" back 

 add threshold = "cut" back
 

 bump version
 

 add lp testing
 

 bug fix use ranks vs stats values
 

 further simplify