oops
 

 Bump version
 

 Bump version
 

 bump 1.3.2
 

 Bump version to 1.3.5
 

 Improve performance by auto-chunking HDF5 writes (#424)

* add auto chunking

* update news

* fix news

* fix linting issue

* Allow manually setting chunk size for HDF5 writes

* update tests

* add test case to confirm

* bump version 

 Handle unnamed `SingleCellExperiment` assays in `as_AnnData()` (#420)

* Automatically name assays in from_SCE()

* Handle NULL values in style_vec()

* Add tests for unnamed SCE assays in as_AnnData()

* Document automatic naming in as_AnnData()

* Style

* fix typo

* add entry to news

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 

 Set up bencher (#423)

* attempt at setting up a bencher

* add devtools as a dependency 

 Bump actions/setup-python from 5 to 6 (#421)

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5...v6)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

 Fix CI (#418)

* wip fix ci

* check python in trycatch

* ncpus isnt used

* use the outputs of the bioc check

* fix ci

* add workaround

* update news

* show output var

* trigger error to verify check results

* undo check

* try to add warning

* alternative warning

* fix documentation

* try to add workaround, move check

* update URL

* alternative fix

* stop vignette if packages are not available

* try installing python

* try with new macos runner

* try with env

* undo workarounds; don't have a fix for mac os 15 intel yet

* attempt another fix

* another attempt

* fix order

* add back to vignette?

* wip

* remove unnecessary code

* remove unused args

* does it help to install python

* disable uv

* wip

* wip

* wip

* update docs

* remove trailing whitespace

* wip

* attempt to fix vignette

* wip

* add info to conf

* attempt to use conda

* does this work

* wip

* add workaround

* simplify renviron

* attempt to fix pkgdown again

* attempt at simplifying r cmd check

* remove cache

* fix python reticulate resolution 

 Separate reading/writing keys in `HDF5AnnData` (#392)

* Add helper functions to read keys from HDF5 files

* Use read_h5ad_element_keys() in HDF5AnnData

Add methods for accessing keys

* Add tests for reading HDF5 keys

* Add write_h5ad_data_frame_index() helper function

* Use helper to write obs/var names

* Style

* Use read_h5ad_element_keys() for obs/var keys

* Roxygenise 

 Add check for 0 dimensions when converting to `Seurat` (#393)

* Add check for 0 dimensions to as_Seurat()

* Add test for converting 0 dim AnnData to Seurat 

 Add issue templates (#395)

* Add issue template config

* Add bug report issue template

* Add feature request issue template

* Add documentation issue template

* Add question issue template

* Adjust issue template formatting 

 warn when rotation is provided, but not in LEM (#407)

 

 Bump actions/checkout from 5 to 6 (#397)

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 

 Fix lint (#389)

 

 Update pkgdown rendering (#379)

* update pkgdown

* update readme

* Update README.md 

 Bioconductor 3.23 devel
 

 Bioconductor 3.22 release
 

 Add release notes (#374)

* Add release notes NEWS.Rd file

* Fix brackets in NEWS.Rd 

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

 version bump
 

 Mac OS OpenMP hell
 

 Update Views properly
 

 Found bug in tests for weight function
 

 Readme other figures
 

 Correct version bump
 

 small additions and tweaks to the DESCRIPTION and vignette
 

 fix for Seurat5
 

 igblastr 1.1.17

Add 'disambiguate.allele.names' argument to install_custom_germline_db().

Many improvements to install_custom_germline_db's man page.

Repair list_IMGT_releases() after the IMGT folks broke our
HTML scrapping code by changing the HTML content of
https://www.imgt.org/download/V-QUEST/archives/
 

 Clean up untracked ..Rcheck files
 

 fix the bugs in database links.
 

 Add explicit Author and Maintainer fields to DESCRIPTION file
 

 Add R check log, package tarball, and test plot outputs to repository
 

 Replace Seqinfo:: with GenomeInfoDb:: namespace imports in NAMESPACE
 

 Add chromInfo parameter to set_seqinfo function documentation and examples
 

 Remove Seqinfo from Imports in DESCRIPTION
 

 Move GenomeInfoDb from Suggests to Imports and add chromInfo parameter support for non model organisms (custom organisms)
 

 Maintainer requested deprecation
 

 minor bug fixes and n_inits as a tunable param
 

 Fixed citation
 

 update maintainer
 

 fix(diann): Add q-value filtering to DIANN big clean function (#11)

 

 Implement DIANN converter for MSstatsBIG. (#9)

 

 update maintainer
 

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
 

 refactor(diann): move q-value filtering to MSstatsClean for DIANN (#116)

 

 fix(diann): Convert zeros to NAs (#114)

 

 Add option to use MS1Quantity for quantifications for Spectronaut (#117)

 

 fix(diann): Update DIANN cleaning to be more memory and speed efficient (#115)

 

 version bump 2.23.5
 

 Bugfix to sanisizer.
 

 CI: use Ubuntu-only with R-devel, bump to 0.99.7
 

 Update CI to R-devel/Bioc 3.23 for R >= 4.6.0, bump to 0.99.6
 

 Bump version to 0.99.4, update R dependency to 4.6.0
 

 devel version bump
 

 v 1.31.1 RC2
 

 merge origin and upstream

Merge branch 'devel' of github.com:jrboyd/seqsetvis into devel

# Conflicts:
#	DESCRIPTION
 

 merge bioc and github

Merge branch 'devel' of github.com:jrboyd/seqsetvis into devel

# Conflicts:
#	DESCRIPTION
#	NEWS
 

 validate view_size valid range on centerAtMax
 

 remove extra curly braces
 

 v bump 1.31.2
finished examples bugfix, missed man files
 

 Merge remote-tracking branch 'bioc/devel'
 

 docs: fix documentation aliases
 

 fix titles for the new data files
 

 Add CE-MS test data files
 

 version bump
 

 Feat/binning transformation (#801)

Co-authored-by: Tuomas Borman <tvborm@utu.fi> 

 Msg (#796)

 

 Fix memory leak. Thanks to Gregory Johnson for finding and fixing ! Closes #44
 

 Removing white space
 

 Updated version number
 

 Adapted the expected outcomes to match new genome build
 

 Update test data to match updated Bioconductor annotations
 

 Updated to use the latest singlepp library. (#302)

This supports efficient processing of sparse matrices and simplifies the code
by eliminating the dependency on knncolle (and thus BiocNeighbors). 

 Forgot to pull down the actual latest version of singler_classic_markers.
 

 igblastr 1.1.14

install_IMGT_germline_db() now also computes and adds "internal data"
to the installed db when 'tcr.db=TRUE' (TR db). Note that, until now,
this feature was only enabled when 'tcr.db=FALSE' (IG db).
Needs more testing.

Implementing the above feature required a complete refactor of internal
function create_region_db(). A major change is that the function now uses
new internal helper clean_allele_set() instead of redit_imgt_file().
The latter is simply an R implementation of the edit_imgt_file.pl script
included in IgBLAST, while the former is a **much** enhanced version of
that. See R/clean_allele_set.R for the details.
 

 # sfi 0.99.4

* `getsfm()` now returns a `SummarizedExperiment` object instead of a `data.frame`, with intensities in the `assay` slot and feature metadata in `rowData`.
* Expanded vignette with "Using the Results" and "Downstream Analysis" sections, demonstrating the `SummarizedExperiment` output.
* Added `SummarizedExperiment`, `S4Vectors`, and `methods` to `Imports`.
* Updated Shiny app and documentation to handle `SummarizedExperiment` from `getsfm()`.
 

 Addressed warning messages
 

 Resolve DESCRIPTION merge conflict
 

 bump 1.2.1
 

 Add the filtering strategy recommended by edgeR and fix the display of the number of features or samples before and after filtering.
 

 Model selection is mandatory for computing contrasts and for integration. The selection of contrasts is required for the differential analysis.
 

 Add a figure showing the missing values during the exploratory step.
 

 removed unrelevant test
 

 removed enrichplot, replaced with ggplot2 and ggnetwork
 

 problem with heatplot -> replace code with ggplot object directly
 

 roxygen
 

 Introduce plotForest (#220)

Co-authored-by: Tuomas Borman <tvborm@utu.fi> 

 P-values to plotBoxplot (#216)

 

 Version 0.99.10
 

 Fix: enforce LF line endings for FASTA to prevent Rsamtools indexing errors on Windows
 

 Update test for pre release version v0.99.9
 

 added scripts and data files of the test data that will be provided with the package and which underlies the paper + add license badge to README
 

 Remove macos-13 in the github action
 

 v0.99.3 test release
 

 Update process_fragment_reads_QC, Change default parameters, Change error in README, Remove stop() in extract_fragment_features
 

 Skip one additional test if ensembl offline
 

 update addBackgroundImage.
 

 Made standard_sequences_only default false
 

 regular maintenance
 

 version bump and news
 

 chore: fix broken tests
 

 chore: fix grid search chart
 

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

 fix: pca loadings plot

only check first element for NULL in label_features
 

 fix: leave-out-out xval

- revise PLS outputs to include y_hat and t_hat
- revise probability calc to work in training/test
- revise balanced_accuracy and add balanced_error
- fix warnings and  add legend to kfold_xval_plot
- update tests
 

 bug fixes and documentationupdate. Vignette has also been updated, along with GitHub workflows and pkgdown website.
 

 v1.3.3
 

 description automerge fix
 

 minor fix
 

 disabled debug output info
 

 Updated random number generator in cellCounts to guarantee real randomness.
 

 bump version
 

 fix: ensure MergeNeighboringPeaksParam merges nested peaks

- Fix a bug with `refineChromPeaks()` and `MergeNeighboringPeaksParam` which
  caused completely overlapping peaks not to be combined if they had the same
  `"rtmin"`, but the first peak had a smaller `"rtmax"` then the second (issue
  #825).
 

 Urgent bug fixes and addition of correct implementation of partial correlation analysis. Relative documentation and test are also included.
 

 Slightly redrawn smoppix figure
 

 Updated version in DESC
 

 Merge pull request #190 from gdrplatform/GDR-3290

 

 doc: reoxygenate
 

 chore: bump version and update NEWS.md
 

 limpa 1.3.7
- New function filterByDetection(), to choose proteins detected in at least a specified number of samples.
- New function EListFromLongFormatFile() to read intensities from a long format file.
  readDIANN() and readSpectronaut() now call this function.
- Argument `run.column` of readDIAN() renamed to `sample.column`.
- Argument `extra.columns` of readDIAN() renamed to `annotation.columns`.
- readDIANN() now longer accepts a data.frame instead of a file.
- Argument `run.column` of readSpectronaut() renamed to `sample.column`.
- Argument `extra.columns` of readSpectronaut() renamed to `annotation.columns`.
- New arguments `isimputed.column` and `censor.value` for readSpectronaut(), making explicit operations that were already built-into readSpectronaut().
- dpcImpute() now gives a deprecation message in favor of dpcQuantByRow().
 

 version bump in news.md
 

 Rebuild documentation

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 

 Speed up mca_core() docstring example

Replaced processing() + dma() pipeline with pre-computed mock CoRe DMA
data. Cuts example runtime from ~38s to ~0.1s.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 

 Speed up metadata_analysis() docstring example

Reduced from 2 examples to 1, subset to 100 rows with 2 metadata
columns, filter constant columns, disabled plot/table saving. Cuts
example runtime from ~47s to ~3s.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 

 Add missing ORGANIZATION field to LICENSE

The BSD_3_clause template requires YEAR, COPYRIGHT HOLDER, and
ORGANIZATION fields.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 

 Bump version: 3.99.38 → 3.99.39
 

 Fix LICENSE file format for R CMD check

R expects the LICENSE file in DCF format (YEAR + COPYRIGHT HOLDER
fields) when DESCRIPTION uses `BSD_3_clause + file LICENSE`. The full
license text is now in LICENSE.md.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 

 bump
 

 bump
 

 bump
 

 version bump 0.99.13
 

 add examples to install_AnVILVRS
 

 version bump 0.99.12
 

 version bump 0.99.11
 

 remove comments redundant with message()s
 

 add ORCID
 

 run download chunk when gcloud is available
 

 regular maintenance
 

 Change of email address
 

 Readme update
 

 checks passed
 

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

 Update documentation of group_by argument in find_de_neighborhoods()

Fixes #26
 

 Added figure
 

 Eye candy
 

 not needed
 

 not needed
 

 Looks nicer with quarto
 

 perhaps the contour plot looks a bit better that way?
 

 some wording changes in the documentation
 

 Some wording improvements
 

 More updates to the vignette
 

 port from Rmd to qmd
 

 Replaced expect_output with expect_message as the former does not work anymore with futile.logger.
 

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

 Ghettofixed for now
 

 Still a problem with predict.scam
 

 Fixed bug in examples in evalweightfunction
 

 Fix gene symbol lookup for Ensembl transcript IDs in newer TxDb

Root cause: TxDb.Hsapiens.UCSC.hg19.knownGene now uses Ensembl transcript IDs
(ENST...) instead of UCSC IDs (uc...). The static gene_symbol.txt lookup table
only mapped UCSC kgIDs to gene symbols, so all gene symbols resolved to NA.

Fix:
- Update .txs2genesym() to handle both UCSC and Ensembl transcript IDs
  - First tries static UCSC lookup table (backward compatible)
  - Falls back to dynamic TxDb + org.Hs.eg.db lookup for Ensembl IDs
- Pass genes TxDb to .txs2genesym() from eventDetection.R
- Add AnnotationDbi to Imports, org.Hs.eg.db to Suggests
- Replace dplyr::as_tibble with as.data.frame for Hits objects
- Clean up vignette diagnostic code
- Bump version to 1.17.5
 

 Added a package manpage.
 

 Remove a file that should not be Git tracked
 

 create hook to identify end of DT rendering for progress() update
 

 add background plot.
 

 version bump 0.99.44
 

 fix line length issue
 

 add section comparing BBS results to dashboard
 

 version bump 0.99.42
 

 chore: drop GitHub ci from bioc
 

 merge PR #15: compatibility for compilation on C++20

feat: compatibility for compilation on C++20 

 ci: fix linux issues with tinytex
 

 ci: fix  missing tex dependency
 

 ci: regenerate updated gha workflows with biocthis
 

 version bump 0.99.41
 

 regular maintenance
 

 regular maintenance
 

 Bug fix for multiple entries in condition_key
 

 Merge pull request #114 from gdrplatform/GDR-3287

Gdr 3287 

 Apply suggestion from @bczech

Co-authored-by: Bartek <32614650+bczech@users.noreply.github.com> 

 bump version
 

 chore: fix vignette chunks
 

 docs: add descriptive and unique chunk labels to all vignettes
 

 revert changes
 

 bump version
 

 fix: move global logic to .onLoad and resolve stack imbalance
 

 inproper merge
 

 Merge pull request #44 from snaketron/fix_get_joint_graph

Fixed two critical bugs in get_joint_graph 

 Merge pull request #46 from snaketron/devel

Devel 

 - last try to get blaster to be working
 

 - added blaster to remotes
 

 Minor adjustments to let checks pass (at least errors and warnings)
- Fixed examples in get_cosine_similarity and get_cdr3_motifs
- Temporary fix: added gglogo to NAMESPACE to avoid some (potentially _gglogo_ package inherent) bug with _ggfortify()_ depending on _data(aacids)_ to sit in the global Environment
- Fixed vignette formatting of User manual groups
 

 - added tests (forgot to include yesterday)
 

 forgot one parameter
 

 merge and push
 

 - Patched get_blosum() to ensure identical clones are linked in graph in edge cases
- Added test-get_blosum.R to testthat
- Version push to 1.9.9
 

 Merge pull request #42 from snaketron/devel

Devel 

 bump version to 1.1.1 for Bioconductor devel
 

 Bump version: 3.99.37 → 3.99.38
 

 fixed crazy variable name `top/Bottom`
 

 removed `seed` from `HelperChecks` (was mandatory argument with no good reason)
 

 docs rebuild
 

 Bump version: 3.99.34 → 3.99.35
 

 removed `VizGraph` `seed` argument
 

 docs rebuild
 

 `VizGraph`: removed `set.seed` and replaced `print` with `plot`
 

 added missing argument descriptions and re-ran documentation
 

 re-ran documentation
 

 re-ran documentation
 

 changed example and re-ran documentation
 

 added plot size options
 

 finalized parameter checks
 

 removed faulty example, changed plot font and re-ran documentation
 

 re-ran documentation
 

 untracking RData and Rhistory
 

 added ggraph dependency
 

 added examples
 

 outsourced parameter checks, enabled seed and made plot edged and nodes look good
 

 outsourced parameter check and added node size option
 

 added support for enrichment result based format
 

 debugging added to cluster_pk, more tests
 

 ran plot tests and printed plots
 

 added function test file
 

 created cluster_pk function
 

 add ebayes
 

 Resolve other issues
 

 UTF-8 to DESCR
 

 fixed a bug in assigning reads to genes w/o considering 'N' in CIGAR.
 

 git clone update
 

 MAINT: Require a minimum version of DFplyr to build the vignette

Also bump the minimum version of R per BiocCheck.
 

 DOC: Add release installation (Bioconductor/Contributions#3986)
 

 CI: Don't clobber R version, etc. in GitHub Actions
 

 Fixed example
 

 Fixed treeplot function as its enrichplot package changed
 

 Fixed treeplot call as it was changed in the enrichplot package
 

 Added a package manpage.
 

 .mm_dream fix: log-transform size factors
 

 Merge branch 'dev' of https://github.com/chain-buds/masstools into dev
 

 Refactor spectrum processing to support Bioconductor Spectra objects (#13)

* Initial plan

* Update vignette to comply with Bioconductor guidelines

Co-authored-by: chain-buds <100484992+chain-buds@users.noreply.github.com>

* Fix tidyverse package reference in vignette

* Fix typo: verctor -> vector in vignette

Co-authored-by: chain-buds <100484992+chain-buds@users.noreply.github.com>

* Fix citation inconsistency in data_sources.txt

Co-authored-by: chain-buds <100484992+chain-buds@users.noreply.github.com>

* Improve comment clarity for interactive function in vignette

Co-authored-by: chain-buds <100484992+chain-buds@users.noreply.github.com>

* Add Spectra package support and conversion utilities

- Add Spectra and S4Vectors to DESCRIPTION Imports
- Create R/spectra_conversion.R with utility functions:
  - df_to_spectra: convert data.frame to Spectra object
  - spectra_to_df: convert Spectra object to data.frame
  - as_spectrum_df: generic converter accepting multiple formats
  - list_to_spectra/spectra_to_list: legacy format converters
- Update NAMESPACE with new exports and imports
- Refactor remove_noise() to support both data.frame and Spectra inputs
  - Maintains backward compatibility with data.frame
  - Detects input type and returns same format
  - Preserves Spectra metadata (precursorMz, rtime)

Co-authored-by: chain-buds <100484992+chain-buds@users.noreply.github.com>

* Refactor ms2_match and get_spectra_match_score for Spectra objects

- Update ms2_match() to accept Spectra objects via as_spectrum_df()
- Update get_spectra_match_score() to accept Spectra objects
- Both functions maintain backward compatibility with data.frames
- Add documentation with Spectra usage examples
- Functions automatically convert Spectra inputs to data.frame for processing

Co-authored-by: chain-buds <100484992+chain-buds@users.noreply.github.com>

* Update deprecated wrapper functions for Spectra support

- Update getSpectraMatchScore() to use as_spectrum_df() converter
- Update ms2Match() to use as_spectrum_df() converter
- All deprecated functions now support Spectra objects
- Maintains full backward compatibility with data.frame inputs

Co-authored-by: chain-buds <100484992+chain-buds@users.noreply.github.com>

* modify some small warnings in copilot agent produced code

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: chain-buds <100484992+chain-buds@users.noreply.github.com>
Co-authored-by: chain-buds <bspchemy@gmail.com> 

 update
 

 CI 

 feat: allow atomic vectors in remove_drug_batch
 

 version bump in devel
 

 fixed the deleting UMI output from step2 UMI merging.
 

 improve unit tests and fix bugs
 

 replace round with as.integer
 

 implement extractCoords as a generic function with methods
 

 update documentation - md files
 

 update citation in README
 

 fixed plyranges dependency on man exmaples