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> 

 Merge for loops
 

 Update snapshot
 

 Deduplicate warnings in read_data()
 

 Do not carry warn value around
 

 minor formatting
 

 submit email on enter key press
 

 - bug correction: logicle transform now uses all (t,m,w,a) parameters.
Previously, t (maximum scale) was always set to a default value hence providing
wrong visualization => this has been corrected.
 

 - bug correction: since version 1.7.2, it was no more possible to display
flowFrames from the scale transformation pipeline part
=> this has been corrected
- updated copyright section to 2026
- bumped version to 1.9.1
 

 bumped version to 1.11.1
 

 updated licence mentions to 2026
 

 updated files for version devel 1.11, Bioc 3.23, R 4.6
 

 Fixes for Limma problem
 

 refactor: update namespace
 

 refactor: update function detection
 

 refactor: update logic for new envision data
 

 refactor: improve logic for supporting combo private prism data
 

 refactor: add support for broad_id
 

 Version number correction
 

 fix bioccheck
 

 Add ORA mode and clarify ORA vs enrichment workflows; bump version to 1.3.1

- Add ORA implementation alongside enrichment mode
- Update README examples for both analysis modes
- Add vignette explaining ORA vs enrichment
- Regenerate docs and update bundled data
- Bump package version to 1.3.1
 

 Merge branch 'master' of https://github.com/myushen/cellNexus
 

 Merge pull request #75 from MangiolaLaboratory/filter-features

Filter features 

 Update rworkflows.yml to remove miniforge version

Remove miniforge version constraint from workflow 

 bypass basilisk in writing h5ad
 

 Refine feature subsetting in get_metacell and related functions. Implement logic to drop experiments missing requested features and emit warnings when samples are dropped. Update documentation across relevant man files to reflect these enhancements.
 

 Enhance get_pseudobulk function to support feature subsetting. Added logic to drop experiments lacking requested features and emit warnings when samples are dropped. Updated documentation to reflect these changes. Added tests to verify functionality for feature subsetting.
 

 Merge pull request #73 from myushen/master

bioconductor package level description 

 maintainer info. package level main page. address timeout
 

 license description, pkg level man
 

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

 Bump version to 1.3.4
 

 replaced author field with Authors@R
 

 Bump to 1.3.3
 

 reduced build time to under 10 minutes
 

 Replace expect_identical with expect_equal
 

 Added countGroupsByBlock(), which wraps table() with normalization by row/column.
 

 Update unit test due to Seurat changes
 

 Add pheatmap to Suggests and bump version
 

 Bump version to 0.99.3

Fix runnable examples requirement for BiocCheck

- Remove if(interactive()) wrappers from all examples
- All 8 exported functions now have truly runnable examples
- Addresses BiocCheck ERROR: 'At least 80% of man pages must have runnable examples'

This resolves the critical BiocCheck failure from the build report.
 

 Docfix for clusterKmeans.
 

 Easier addition of columns before/after defaults in previewMarkers.

Sometimes we just want to add a single column to the defaults (e.g., gene
symbols) without having to explicitly re-specify all of the defaults.
 

 IRLBA seed should be a double when passed to C++ code.
 

 Fixes to the tatami delayed log bindings.
 

 Updated vendored libraries, added kmeans_tatami.
 

 Added further documentation
 

 formatting fix
 

 Fix Seurat function arguments

Change 'slot' argument to 'layer' in Seurat function calls. The use of 'slot' was deprecated and now has been defunct. This caused errors when running the selectTargetGenes() function.
 

 Add pkgdown site and GitHub Pages deploy
 

 Add funding info and minor formatting tidy
 

 fix bioconductor build errors

- Update LICENSE to DCF format required by R packages
- Add proper license declaration (MIT + file LICENSE)
- Add VignetteBuilder and vignette dependencies to DESCRIPTION
- Reorganize dependencies: move SummarizedExperiment to Depends, remove unused imports
- Add proper vignette metadata for indexing
- Add error handling in .onLoad for OSF network calls
- Import SummarizedExperiment in NAMESPACE
 

 version bump
 

 syncing bioc and GH
 

 Replace ggalt with ggforce
 

 Merge pull request #84 from alanocallaghan/flip-arg

Add flip arg to silence 'Coordinate system already present' 

 Merge pull request #74 from LTLA/tatami-v3

Updates for the v3 tatami interface. 

 Add flip arg to silence 'Coordinate system already present'
 

 Added assorthead to the pile of includes.
 

 Minor code reorganization for some future-proofing.
 

 Merge pull request #64 from LTLA/tatami

Migrate matrix shuffler to the new tatami C++ API. 

 Added some ignore files to avoid committing the binaries.
 

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 

 chore(deps): update jamesives/github-pages-deploy-action action to v4.8.0 (#180)

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

 Mention default port change in NEWS
 

 Enable coalesce_linter
 

 Update
 

 feat: add new addJoinDefinition function

- Add the `addJoinDefinition()` function that allows to integrate newly added
  database tables automatically into queries.
 

 Add hardcoded support for "experiment" table
 

 Bump version
 

 update readme
 

 trying again to avoid timeout
 

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

 Update
 

 limpa 1.3.3
- dpcImpute() renamed to dpcQuantByRow().
- dpcQuantByRow() now longer outputs NPeptides column
- Two new sections in vignette linking to several external vignettes, FAQ and Reference Manual.
- Remove DIANN3Species.Rmd as internal vignette, in favor of external vignette.
- dpcQuant() now drops protein ID column in favor of row.names.
- dpcQuant() now stores the DPC and the hyperparameters in the output EList object.
- simProteinDataSet() now stores dpc in output object.
- New argument `las` for plotProtein() and plotPeptides().
- plotPeptides() now plots sample names, same as plotProtein().
- The y-axis from plotPeptides() is now labelled "Log-intensities".
- Update NEWS.Rd.
 

 Fixed conflicts in version change
 

 Update cytofQC.Rmd
 

 update the scores on the initial functions and the documentation.
 

 fixed plyranges namespace
 

 fix: specify minimum r version
 

 fixed dependency
 

 Slightly improved wordings
 

 I add setting the random seed in the unit test 'tests/testthat/test_calib.R', to avoid (very rare) situations in which the optimization does not converge, and which have nothing to do with the test's objective.
Also, removed a few lines of now superfluous code in vsn2.c
 

 update prepareRMSK() using AnnotaionHub
 

 - Add built-in germline db _AIRR.rhesus_monkey.IGH+IGK+IGL.202601

- Rename translate_V_alleles()'s argument 'region' -> 'V_segment'.

- Add makeogrannote(), a function to extract V gene FWR/CDR annotations
  from an OGRDB JSON file.
 

 fix for updateMetadata and CharacterList
 

 v1.23.2 -- accepted @lahuuki's PR #119.
 

 Merge pull request #119 from LieberInstitute/enrichment_list_genes

List overlapping genes in gene_set_enrichment 

 v1.23.1 -- fetch_data() now allows downloading LFF_spatial_ERC files thanks to @lahuuki and https://github.com/LieberInstitute/spatialLIBD/pull/118
 

 mostly auto-reformat code with air
 

 Merge pull request #118 from LieberInstitute/add_ERC_data

Add LFF_ERC_spatial data to fetch_data() 

 Update docs
 

 Update fetch_data with ERC dropbox links
 

 Add ERC 8 type opttions to fetch_data()
 

 Add broad level pb and modeling data too
 

 Add metadata file for spatial ERC
 

 Version bump