merge upstream divergence
 

 bump version to 1.15.1
 

 fix Rd documentation warning for L1_module_data_space and L1_module_result_space
 

 Merge upstream/devel into devel and resolve version conflict
 

 Update module_triselector.R

Last selector in triselector is on server side
 

 add new module for batch comparison of variable - selected vs non-selected
 

 Update module_ora.R
 

 add tags for AI browser
 

 Delete module_triselector.R.bak
 

 improve reactive chain 1
 

 remove codes commented out
 

 feat: replace magic numbers with named constants

 - Create R/constants.R with 40+ application constants
  - Update 12 R files to use named constants
  - Improve code readability and maintainability
  - Constants organized by category (API limits, UI, stats, etc.)
 

 chore: bump version to 0.99.12
 

 Merge branch 'devel' of https://github.com/AhmedSAHassan/DoReMiTra into devel
 

 added missing manpage for the new function
 

 fixed one tiny missing import for the assignment to colData
 

 adjusting section title
 

 bump version
 

 Resolve merge conflict in README.md
 

 update description
 

 update vignette
 

 docs: Weekly AI doc upgrade for `cytoscapeNetworkOutput` (#77)

 

 fix the readme title.
 

 feat: Enable support for ThermoFisher raw instrument file reading (#20)

Replace direct mzR calls throughout the codebase with a new S4-based
  reader abstraction (`R/raw-file-reader.R`) that decouples the package
  from any single file-reading backend.

  New S4 class hierarchy:
  - `MsRawReader` — virtual base class defining the reader interface
  - `MzrReader` — wraps an open mzR connection for standard open formats
    (.mzML, .mzXML, .CDF)
  - `RawrrReader` — wraps a file path for ThermoFisher .raw files via
    the rawrr package (added to Suggests)

  New generics (all defined in raw-file-reader.R):
  - `ms_header(reader)` — returns a normalised scan-header data.frame;
    for CDF files the BPC/TIC values are computed from raw peaks inside
    the method, removing the special-case branch that previously lived in
    `create_bpc_tic()`
  - `ms_peaks(reader, scans)` — always returns a list of matrices, even
    for a single scan, so callers use `[[1]]` consistently
  - `ms_close(reader)` — closes the backend connection (no-op for
    RawrrReader)
  - `ms_chromatogram(reader, mz, ppm, rt_range)` — native XIC extraction
    (RawrrReader delegates to rawrr::readChromatogram(); MzrReader raises
    an informative error)
  - `open_raw_reader(path)` — factory function that dispatches by file
    extension

  Internal changes:
  - `R/io-raw-data.R` deleted; its two helpers (`io_get_raw_data`,
    `io_close_raw_data`) reimplemented in raw-file-reader.R using the new
    abstraction
  - All scattered `mzR::header()`, `mzR::peaks()`, `mzR::openMSfile()`,
    and `mzR::close()` calls in constructors-chromatograms.R,
    constructors-spectra.R, creators-chromatograms.R, creators-spectra.R,
    and creators-intensity-map.R replaced with the new generics
  - `create_chromatogram()` now branches on reader class for XIC: uses
    `ms_chromatogram()` for RawrrReader and the existing scan-by-scan loop
    for MzrReader
  - Guard added in `creators-chromatograms.R` so that empty mass_traces
    are never rbind-ed (fixes potential zero-row data.frame issues)
  - `lcmsPlot()` default BPPARAM changed from `BiocParallel::SerialParam()`
    to `NULL` to avoid creating unnecessary parallel workers by default
  - Test helpers updated to return `MzrReader` objects
  - Vignette updated with .raw file examples (eval=FALSE) and removal of
    now-redundant ppm/rt_tol arguments from BPC/TIC examples 

 Bump version to 0.99.3
 

 makeTxDb now imported from txdbmaker package
 

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

 delete ds store
 

 Bump version to 0.99.2
 

 fix vignette typo
 

 Bump version: 0.99.9
 

 Ignore .Rproj file
 

 update weights
 

 Solve voronoi issue
 

 Vignette writing
 

 Wasserstein function returns a value
 

 Edit coding style in testing
 

 Edit coding style
 

 Edit .Rbuildignore
 

 Reduced check time
 

 refactor: use `data.table::rbindlist()` to combine `data.frame`s

- Use the `data.table::rbindlist()` instead of `MsCoreUtils::rbindFill()` to
  merge spectra data `data.frame`s. This should improve the performance of
  `spectraData()` on the `MsBackendPy` and for the conversion of Python data
  structures to `Spectra`.
 

 ci: update to BioC devel
 

 Update DESCRIPTION file
 

 Bump version for Bioconductor resubmission
 

 Reduced vignette execution time
 

 bump version after remove tracking tests/DS_Store
 

 fix errors in bioc build, bump version
 

 update description to remove author, maintainer fields
 

 Minor vignette edits
 

 bump version number
 

 add inst folder
 

 remove tests for slices,alpha,maxDirections since not needed
 

 add test files and other minor changes
 

 build
 

 remove energy bcdc from linh
 

 remove gsl from description (since not used anywhere)
 

 add gsl to description
 

 test text
 

 extra text as test
 

 include ... param description
 

 fix to examples
 

 remove RFast
 

 fixes to bcdc
 

 remove rproj
 

 create placeholder for analysis codes
 

 create test file for createWeightMatrix
 

 update project
 

 fix typos
 

 remove need for removed code
 

 try making x numeric
 

 increase indent, use -> for assignment, add BioC install instructions
 

 use Authors@R in DESCRIPTION
 

 Merge branch 'devel' of github.com:saezlab/OmnipathR into devel
 

 added import roxygen strings
 

 changed metabolite id from list to char vector
 

 re-ran documentation
 

 using devel request for now
 

 removed requests package completely
 

 deleted old commented-out code
 

 added reactome functions
 

 include `CLAUDE.md`
 

 fixed case with non-existing colnames in `cast_logicals`; +short version of intercell field names
 

 Fixed typo in vignette for BioC
 

 Addressed warning messages
 

 add weekly readme updater (#78)

 

 refactor(networks): Refactor visualization suite to enable download of PNG files (#173)

 

 add curation filtering on Shiny for network interpretation (#121)

 

 feat(converters): Add Metamorpheus PTM Converter (#158)

 

 Add Metamorpheus to MSstatsFormat Converter into Data Upload Tab (#154)

 

 add checkboxes for dose response curves for log transformation and increasing assumption (#153)

 

 docs(statmodel-ui): Add text illustrating what -1 and 1 mean for contrast matrix (#150)

 

 add LongRead
 

 Update DESCRIPTION file
 

 Update DESCRIPTION file
 

 Added function to convert to bsseq
 

 Final JOSS fine-tuning 

 Add compatability for negative value Features
 

 bumping up the version
 

 adding a test to the new function
 

 expanding the information of the function output
 

 add author column in the metadata output
 

 message the output instead of printing
 

 correcting the information on how the function filters
 

 add a function to list metadata fields of the DoReMiTra collection
 

 adding the info about tissue manually
 

 removing unneccessary text
 

 adding the info about the tissue
 

 updating the function to include info about the tissue
 

 updating the metadata to contain info about the tissue
 

 updating the metadata information for the SE objects to contain information about the tissue
 

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

 changing the sys.date to biocStyle
 

 added entry in gitignore
 

 adding 'basic' feature
 

 Final JOSS fine-tuning 

 Add compatability for negative value Features
 

 adding 'basic' feature
 

 Final JOSS fine-tuning 

 Final JOSS fine-tuning 

 Merge pull request #4 from jromanowska/paper-corrections

Update paper.md 

 Merge pull request #115 from gdrplatform/GDR-3299

Gdr 3299 

 refactor: update as per review
 

 test: add unit tests
 

 adding doi in citation
 

 adding citation and fixing DESCRIPTION
 

 refactor: use data.table::rbindlist to merge data.frame

- Use `data.table::rbindlist()` instead of `rbindFill()` to merge the
  `data.frame`'s for the individual spectra.
 

 Merge pull request #21 from rformassspectrometry/jomain

fix: ensure results are data.frame 

 Minor documentation changes
 

 ci: update cache version
 

 Update NEWS
 

 refactor: use `data.table::rbindlist()` to combine data.frames

- Use `data.table::rbindlist()` in `readMsp()` to combine the `list` of
  `data.frame` (i.e., spectra). This improves performance, in particular
  for large MSP files with many spectra or import from a large number of
  individual MSP files.
 

 refactor: include r_squared in PCR results

Includes regression_type and r_squared in the subset of metadata copied
from fit models to the experiment colData by determinePCRResults().
Also refactors the determinePCRResults() function for modularity and
readability.
 

 remove the print message.
 

 bump version to 1.11.2
 

 Update test_function_calculateMetrics_from_Spectra.R
 

 Update test_function_calculateMetrics_from_Spectra.R
 

 Update test_function_calculateMetrics_from_Spectra.R
 

 Update test_function_calculateMetrics_from_Spectra.R
 

 Update test_function_calculateMetrics_from_Spectra.R
 

 fail tests
 

 Update test_function_calculateMetrics_from_Spectra.R
 

 Update test_function_Spectra_qualityMetrics.R
 

 Update test_function_calculateMetrics_from_Spectra.R
 

 Update test_function_calculateMetrics_from_Spectra.R
 

 fix typos in function call
 

 add MsDataHub to IMPORTS
 

 Deprecate

 - responded cannot maintain after large file requests
 

 User requested on bioc-devel
 

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_21 branch
 

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

 bump x.y.z version to odd y following creation of RELEASE_3_19 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_18 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_17 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_16 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_15 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_14 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_13 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_12 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_11 branch
 

 bump x.y.z version to odd y after creation of RELEASE_3_10 branch
 

 bump x.y.z versions to odd y after creation of RELEASE_3_9 branch
 

 updated library spectra
 

 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
 

 bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch
 

 bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
 

 Edited paper for JOSS submission
 

 refactor: add the code change
 

 refactor: use `data.table::rbindlist()` for HMDB spectra import

- Use `data.table::rbindlist()` for the import of HMDB spectra increasing its
  performance.
 

 fixing export function example
 

 styling
 

 changing the export function behavior, it's now possible to export the available assays in dde along with dea and fea results
 

 update description and namespace
 

 updating vignette
 

 added helper function to export results stored in a dde obj as excel files
 

 Changes after Bioconductor review
 

 Add 'source_set' argument to download_OGRDB_germline_sequences()
 

 refactor: use `data.table::rbindlist()` instead of `do.call(rbind)`

- Replace `do.call(rbind,...)` calls with `data.table::rbindlist()` for
  combining `data.frame`'s improving performance for larger data sets.
 

 Refactor internal utility igblastr:::download_V_ndm_data_from_OGRDB()
 

 version bump in devel
 

 bump version
 

 air formatting
 

 remove some function
 

 update gsub usage
 

 update documentation
 

 fix check_indices bug
 

 0 indices are not checked if the indices are sequential
 

 fix vignette
 

 update indexing approach for [ and crop methods
 

 small fixes
 

 initial implementation of index checks
 

 update file paths and zarr utils checks
 

 update vignette
 

 edgeR 4.9.3
- New function DGEListFromTximport().
 

 Bump package version from 1.3.2 to 1.3.3 

 chore(visualizeNetworks): Remove dependency on cytoscapeDesktop (#75)

 

 Changes to fix warnings
 

 Fix the issue for idconv
 

 feat: implement Shiny web application

Adds a web application implemented in Shiny to the package, providing
access to the core workflow without requiring programming experience.
 

 Finalised JOSS review comments
 

 Cleaned up workflows
 

 Update main.yml 

 Update draft.yml 

 Some fine-tuning in-line with JOSS review 

 Some fine-tuning in-line with JOSS review
 

 Edited paper to accomodate editor's comments
 

 Some fine-tuning in-line with JOSS updates
 

 Incorporating comment from JOSS editor
 

 Merge branch 'master' into devel
 

 1.55.2 additional BioC style fixes

https://github.com/joey711/phyloseq/issues/1796
 

 Updated all libraries to their latest versions.
 

 Updated NEWS.md and bumped-up version

Last fixes
 

 Bump to 1.3.6
 

 Add test_request to missed functions in test
 

 Remove check.list top-level file as requested by Bioconductor
 

 image workflow clean
 

 Skip long workflow test on Bioconductor
 

 Add proper @return sections to VCF IO functions
 

 Skip long workflow test on Bioconductor and move R.utils to Suggests
 

 trigger build
 

 Minor C++ warning fix for unused variable.
 

 Move BiocParallel to Suggests to cut down on dependencies.
 

 v1.55.1 build fix diffusion

https://github.com/joey711/phyloseq/issues/1796
 

 1.54.1 appears to pass build check

https://github.com/joey711/phyloseq/issues/1796
 

 1.54.1 more unit test fixes and roxygen rebuild
 

 1.41.1 fix url complaint warning in linux build
 

 Version bump to 0.99.6 and trigger rebuild (Bioconductor/Contributions#4054)
 

 refactor(visualizeNetworks): Add new module for visualizing networks (#72)

 

 Update links to `{pkgdown}` site (#429)

* Update links to {pkgdown} site

* Fix links

* Update README.md

Co-authored-by: Philipp A. <flying-sheep@web.de>

* remove old link

* fix link

* bump version

* fix broken link

* remove duplicate link

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
Co-authored-by: Philipp A. <flying-sheep@web.de> 

 Bump actions/github-script from 7 to 8 (#426)

Bumps [actions/github-script](https://github.com/actions/github-script) from 7 to 8.
- [Release notes](https://github.com/actions/github-script/releases)
- [Commits](https://github.com/actions/github-script/compare/v7...v8)

---
updated-dependencies:
- dependency-name: actions/github-script
  dependency-version: '8'
  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> 

 Change url and ref
 

 Modernize CITATION
 

 Bump version to 0.99.1 and add R.utils to Imports
 

 remove trailing spaces
 

 remove trailing spaces
 

 Merge branch 'devel' of https://github.com/tnaake/MsQuality into devel
 

 Merge pull request #20 from hechth/uri_bugfix

added conversion to uri from local file to the export function 

 Update check-bioc.yml
 

 Update check-bioc.yml
 

 Update check-bioc.yml
 

 Update check-bioc.yml
 

 Update check-bioc.yml
 

 added conversion to uri from local file to the export function
 

 Modernize citation

- Use bibentry() rather than citEntry()
- Use c.person() rather than personList()
- Remove redundant textVersion()
 

 + OpenMP on Windows
 

 fix: use serial backend for BiocParallel in vignettes
 

 fix: add missing function to _pkgdown.yml
 

 add molecule module.
 

 deprecation(groupComparisonPTM): Deprecate data.type parameter (#124)

 

 Enable PTM site-level visualization (#69)