Fix on the handing of missing data with the GSVA method. Bug reported in issue #257.
 

 fix: remove the conflicting import for dplyr::rename 

 bump version
 

 cleanup code
 

 bug fixed #339
 

 changes according to #335
 

 Add fc_threshold parameter to cnetplot for filtering genes by fold change

Add new fc_threshold parameter that filters genes to only include those
with absolute fold change greater than the threshold. This allows users
to plot only genes with |foldChange| > fc_threshold (e.g., fc_threshold = 1).

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
 

 Merge pull request #1 from ivokwee/fix-treeplot-sizecolor

add size_var; fix color 

 Fix reversed colors in heatmap plot: add REVERSE=FALSE
 

 change sorting
 

 bump version
 

 add runnable examples, add demo bisseq file, fix note for lazy data
 

 add fnd role
 

 update R to 4.5.0
 

 add seqlevels_style and bam_output_dir
 

 Merge branch 'dev' into devel
 

 Update code in response to changed exports from plyranges.
 

 chore: Merge pull request #168 from CogDisResLab/fix/dfplyr-name-collision

 

 style: ensure that other lints are addressed 

 test: update the argument order in fliter signature 

 rename directory
 

 add info on annotation
 

 rename function
 

 add getExonicReads
 

 save TxDb
 

 add getExonicReads
 

 add getExonicReads
 

 Fix a minor bug at a code to use seqOptimize().

Merge branch 'RELEASE_3_22'

# Conflicts:
#	DESCRIPTION
#	inst/NEWS.md
 

 Fix a minor bug at a code to use seqOptimize().
 

 version
 

 widen the range for `which` in the BigBed example
 

 version
 

 Merge pull request #178 from gdrplatform/time-course

feat: add support for the `time-course` experiment 

 build: trigger build
 

 Update NEWS.md

Co-authored-by: gemini-code-assist[bot] <176961590+gemini-code-assist[bot]@users.noreply.github.com> 

 Merge pull request #184 from gdrplatform/time-course

Time course 

 feat: switch to log2 in time-course normalization
 

 refactor: improve data_model.data.table (time-course case)
 

 refactor: and bugfix normalize_SE_time_course
 

 refactor: create_SE (time-course)
 

 Update R/normalize_SE.R

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com> 

 Merge branch 'main' into time-course
 

 chore: bump v+c
 

 Update R/normalize_SE.R

Thanks @j-smola, this change looks good

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com> 

 Update R/create_SE.R

Thanks @j-smola, yes, we can definitely swap out the lapply. with gDRutils::loop.

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com> 

 Update R/create_SE.R

Thanks @j-smola, yes, we should add the gDRutils:: prefix.

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com> 

 Added Functions for Loading Incucyte Live-Cell Imaging Data as SummarizedExperiment
 

 Updated SE to be compatible with time-course live cell imaging data
 

 Add the QLF test
 

 Fix warning with pvalues
 

 version and date
 

 fix deployment from sandbox branch
 

 change maintainer
 

 Update README to include BigOmics link 

 Merge pull request #5 from bigomics/merge-dualgsea

merge dual_test and dualGSEA . Update tests and vignette 

 wip
 

 update message
 

 remove use.rank in function doc
 

 remove use.rank option
 

 small fix align pv; add maxp method
 

 Fixed issue introduced by switching underlying binding profiles to GRanges
 

 Updated to damidBind 0.99.8
 

 Trying again to remove any unicode issues
 

 small update to documentation
 

 update class
 

 update more documentation
 

 update vignette
 

 update R buildignore
 

 update documentation
 

 more bioc updates
 

 update HDF5DataFrame to take path and name as arguments only
 

 Bump version
 

 Bump version
 

 Create zstd-1.5.7.patch
 

 Use custom Makefile
 

 Change version
sdf
 

 version
 

 version and date
 

 Merge pull request #108 from gdrplatform/time-course

Time course 

 chore: improvements
 

 chore: simplify incucyte helper function
 

 refactor: improve logic for Incucyte loader
 

 Merge branch 'main' into time-course
 

 chore: minor correction
 

 refactor: `load_results_Incucyte` function
 

 chore: minor improvements
 

 feat: refactor `load_results_Incucyte`
 

 Merge branch 'main' into time-course
 

 Apply suggestion from @j-smola

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com> 

 Apply suggestion from @j-smola

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com> 

 test: fix warnings/notes
 

 Updated incucyte machine file loading
 

 Updated to 0.99.7
 

 Updated installation instructions
 

 Updated labelling details
 

 Sample adjustment wasnt in documentation yet
 

 Fix in fetching rows from SVT_SparseArray matrices
 

 Removed minimizing geneset again as it didnt add much. Aligned samples in examples and test
 

 update af_prediction() unit test

- expected table columns match those returned
 

 Version bump
 

 and removed plyranges from namespace
 

 Correction due to updates lme4
 

 version bump, 1.7.1
 

 Merge pull request #28 from AnnekathrinSilvia/revision_improvements

Revision improvements 

 Fixed typo
 

 Added the new path_to_GeDi funciton to the vignette
 

 Changed the path_to_GeDi function to expect a data.frame for all enrichment packages
 

 Added the info on the new path_to_GeDi function to the NEWS file
 

 Finished documentation for the new function
 

 Restructured the table below the clustering graph to now also reflect graph metrics such as betweenness, centrality and other graph measurements
 

 Removed old kappa implementation and renamed the new, more efficient one to make sure that the app still runs correctly
 

 imports fixed in the code of the specific functions
 

 Merge branch 'revision_dh' of github.com:AnnekathrinSilvia/GeDi into revision_dh
 

 Resolved merged conflicts in clustering_wordcloud.R

Merge branch 'revision_dh' of https://github.com/AnnekathrinSilvia/GeDi into revision_dh

# Conflicts:
#	R/clustering_wordcloud.R
 

 updated the news in the upcoming devel version
 

 Merge branch 'revision_dh' of github.com:AnnekathrinSilvia/GeDi into revision_dh
 

 Decoupled the option to filter generic terms and individual terms in the wordcloud implementation. Also made the generic terms a global variable.
 

 Implemented a revised goDistance funciton using the simona package
 

 Added the option to filter generic terms from the wordcloud.
 

 finished round on the meet min matrix calculations
 

 full go at the kappa distance implementations
 

 adding all different flavors on the jaccard distance functions
 

 fixing the example
 

 added manpages for the now internal functions
 

 adding documentation for the internal .map_to_color
 

 removing unrequired mention in the vignette
 

 map2color to internal .map_to_color
 

 updated required roxygen version to the latest
 

 [packages] replaced by `packages` to avoid the note
 

 updating GHA to a more recent cache version
 

 refactor: appease lintr
 

 ci: trigger build
 

 test: update unit tests
 

 refactor: update as per review
 

 doc: update documentation
 

 doc: bump version
 

 R dependency >= 4.6.0 reflecting new Bioconductor release and minimized
geneset of scRNAseq for quicker vignette/examples
 

 docs: the README file has been updated.
 

 Updated to v0.99.6
 

 Updated tests
 

 Added new `cond` logic and negative occupancy loci filtering.
 

 Fixed example for new `cond` logic.
 

 Fixed example for new `cond` logic.
 

 Removed FDR universe filtering (replaced by more appropriate low-signal filtering earlier in the pipeline)
 

 Updated to v0.99.6
 

 Merge pull request #266 from lmweber/estella

Estella 

 change link to landing site
 

 Merge pull request #15 from estellad/vhdcellsegread

Vhdcellsegread 

 Merge pull request #263 from lmweber/everev

evening revision 

 rmv local env
 

 Merge branch 'sandbox' of https://github.com/estellad/PrinciplesSTA into sandbox

get updates
 

 revise acknowledgments
 

 suppress ggplot-related messages/warnings
 

 fix VisHD cross-refs
 

 fix typo -.-
 

 fix #260
 

 Merge pull request #259 from lmweber/downtime

add tryCatch to SpatialLIBDB part 

 Merge pull request #258 from lmweber/downtime

skip tx.parquet retrieval 

 Merge pull request #256 from lmweber/merge_sandbox

Merge sandbox 

 rmv superfluous subheader
 

 dplfc revision
 

 seq-qc revision
 

 fix messages/warnings/verbosity
 

 add box on theory & PCR; add references
 

 fix typo
 

 Merge pull request #246 from lmweber/vhd

Workflow: Visium HD (segmented) 

 alter fig sizing
 

 fix typo
 

 fix msigdbr-related warning
 

 revise wording; remove caching
 

 Merge pull request #245 from lmweber/refs

`apx-citation` draft 

 add bin/cell overlay nuc cell polygons
 

 Merge branch 'lmweber:sandbox' into sandbox
 

 Merge branch 'sandbox' into vhd
 

 change symbols
 

 retrigger
 

 couple more words on QC
 

 w/o superscripting
 

 fix symbols
 

 trigger deploy from sandbox
 

 Merge branch 'sandbox' into refs
 

 fix 'incomplete final line' warnings
 

 add note on cache invalidation
 

 fix giotto ref
 

 revise wording
 

 +vhd-seg draft
 

 split vhd bin/seg
 

 Merge branch 'lmweber:sandbox' into sandbox
 

 added infrastructure refs
 

 add missing final lines
 

 fill missing entry
 

 add citation draft
 

 Merge pull request #13 from estellad/vhdcell

remove tidyverse from DES 

 testing Marcel reader
 

 Add Taxonomy ID to TxDb object returned by makeTxDbFromEnsembl() (#13)

Like for other makeTxDbFrom* functions, the new 'taxonomyId' argument of makeTxDbFromEnsembl() is set to NA by default. So if the user doesn't supply a Taxonomy ID via the argument, GenomeInfoDb:::lookup_tax_id_by_organism() is used to retrieve the taxonomy ID for the supplied 'organism'. Otherwise GenomeInfoDb:::check_tax_id() is used to check the user-supplied taxonomic ID. 

 BSgenomeForge 1.11.1: Fix issue in internal helper drop_rows_with_NA_accns()
 

 update package version
 

 Remove plyranges dependencies
 

 1.41.1
 

 stash
 

 style: fixed minor style issues 

 style: convert all pipes to |> 

 test: remove the unnecessary failing test 

 test: remove the httptest2 style test files
 

 feat: remove the is_L1000 column
 

 fix: don't import dplyr::desc to avoid collision warning
 

 feat: align consensusConcordants and its tests with the rest of the package
 

 feat: update the system data for l1000
 

 fix: add different cases to generate dummy data
 

 test: simplify the test helpers
 

 docs: add missing docs for helper functions

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
 

 tests: add httptest2 tests for getConcordants
 

 tests: add httptest2 for better mocking
 

 feat: improve and modularize getConcordants
 

 build: update renv dependencies
 

 chore(deps): update actions/checkout action to v5.0.1 

 chore(deps): update actions/upload-artifact action to v5 

 chore(deps): update r-lib/actions action to v2.11.4 

 chore(deps): update actions/checkout action to v5 

 chore(deps): update actions/checkout digest to 08eba0b 

 chore(config): migrate config renovate.json 

 chore(deps): update pre-commit hook compilerla/conventional-pre-commit to v4.2.0 

 docs: update the path to the pdf file for the joss paper
 

 ci: remove the graphite check-ci action
 

 build: update the pre-commit config
 

 fix: fix syntax error in DESCRIPTION file
 

 build: update renv dependencies
 

 feat: add the structure of the joss paper
 

 build: update the gitignore file and renv
 

 chore(deps): update r-lib/actions digest to bd49c52 

 chore(deps): update actions/upload-artifact digest to 4cec3d8 

 chore(deps): update r-lib/actions digest to 14a7e74 

 fixed unit tests with new version of ggplot2
 

 updated version in NEWS.md to 1.7
 

 updated licence file and statements in R files to 2025
 

 bumped version to 1.5.0 (Bioc 3.22)
 

 log message with `OmnipathR` version from `metaproviz_init` and `equivalent_id`
 

 update r/bioc versions
 

 SparseArray 1.11.5: Various improvements

o Rename internal helper subset_SVT_by_Nindex() -> .subset_SVT_as_SVT()

o Revisit and optimize implementation of extract_array() method for
  SVT_SparseArray arrays. Old implementation was doing:

      as.array(.subset_SVT_as_SVT(x, index))

  New implementation is based on new internal helper .subset_SVT_as_Rarray()
  which avoids the intermediate SVT_SparseArray representation. With these
  improvements, extract_array() is now 3 to 4 times faster than in BioC
  3.22.

o Extracting a single row from an SVT_SparseMatrix object 'x' with

      x[i, ]

  is now 15% to 20% faster.

o Add unit tests for .subset_SVT_as_SVT() and .subset_SVT_as_Rarray().

o Speed up nzvals() on SVT_SparseMatrix objects and nnavals() on NaArray
  objects by overriding the default methods with specific methods
  implemented in C. This yields a 15x to 20x speedup.
 

 Fix ggplot unit() usage in pred_ensembel; harden calculateBE; bump version
 

 Merge pull request #162 from seandavi/copilot/fix-getgeo-error

Fix parseGSEMatrix crash on files with irregular metadata lines 

 Add NEWS entry for GSE425 parsing fix

Co-authored-by: seandavi <92435+seandavi@users.noreply.github.com>
 

 Initial plan
 

 Turn off single-cell eval to check GH actions
 

 Merge branch 'devel' of https://github.com/seandavi/GEOquery into devel
 

 Add Quarto setup action to pkgdown workflow 

 Update branches for pkgdown workflow 

 add citation.
 

 Fix unit test
 

 v1.3.1: Fix ssBC, 1-sample mode; sync docs