c++11->c++17
 

 Update maintainer from Jessica Anderson (formerly McClintock) to Evan Johnson
 

 Merge pull request #141 from jessmcc22/devel

Changed maintainer 

 Change maintainer from Jessica Anderson to Yaoan Li
 

 Update bioconductor version number
 

 "size" aesthetic in geom_line is depricated in ggplot, replaced by "linewidth"
 

 Added parameter to manually shift accepted range in RemoveDoublets.
 

 Increased version number for RemoveMargin changes
 

 Added channel selection for min and max margins in RemoveMargins + added an attribute ("margin_matrix") to the resulting flowframe with the margin counts
 

 Remove subset in BuildTimePlot
 

 Streamlined generation of the package manpage.
 

 ci: don't fail macOS build if xquartz download is unavailable

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

 correct double threshold logic in reduce_solution_network_double_thresh
 

 Merge pull request #86 from rformassspectrometry/jomain

feat: add beta_values function 

 ci: use R devel
 

 Version bump
 

 add Makevars file
 

 Adapt to new testthat behaviour (#87)


* Update to new BioC release versions

* remove set seed and test properly the result function

* bump version to 1.28.1

---------

Co-authored-by: Felix Brechtmann <37140213+brechtmann@users.noreply.github.com>
Co-authored-by: Christian Mertes <mertes@in.tum.de> 

 Version bump: bug fix
 

 move use_germline_db() and use_c_region_db() to their own .R/.Rd files
 

 fixed typo in README
 

 Merge pull request #6 from feargalr/devel

updated readme with examples of taxonomically defined set analysis 

 updated readme with examples of taxonomically defined set analysis
 

 Updated runWF example
 

 Merge branch 'release' of https://github.com/biobakery/Maaslin3 into release
 

 Merge pull request #39 from andrewGhazi/misc

Miscellaneous small changes 

 Merge pull request #38 from andrewGhazi/suggestSE

move (T)SE to Suggests. check_installed() where needed. Add test to c… 

 add reformulas dependency to avoid warning from lme4
 

 move (T)SE to Suggests. check_installed() where needed. Add test to check ability to read SEs.
 

 Merge pull request #37 from biobakery/devel

Change prevalence max to 1.01 

 Update maaslin_plot_results_from_output.Rd 

 Merge pull request #36 from biobakery/devel

Devel 

 Update LICENSE 

 Update README.md 

 Merge pull request #33 from biobakery/devel

Updated object size function 

 Merge pull request #31 from biobakery/devel

Fixed formulas with feature specific covariates, fixed rownames in tibbles 

 Merge pull request #28 from biobakery/devel

Devel 

 Merge pull request #26 from biobakery/devel

Devel 

 Merge pull request #22 from biobakery/devel

Update utility_scripts.R 

 Merge pull request #20 from biobakery/devel

Fix ordered/group data frame joining 

 Merge pull request #18 from biobakery/devel

Allow arbitrary naming in tables, add null_hypothesis, add preprocess_taxa_mtx 

 Merge pull request #15 from biobakery/devel

Version 0.99.4, not 1.0.0 for Bioconductor 

 Merge pull request #13 from biobakery/devel

Updated min_abundance manuals 

 Merge pull request #11 from biobakery/devel

Update DESCRIPTION 

 Merge pull request #9 from biobakery/devel

Update maaslin3.R 

 version bump
 

 SpaceTrooper utilities vignette, README fixing
 

 Add taxon_rank_sets helpers and tests
 

 fixing website navbar
 

 Merge devel into main (resolve vignette rename conflict)
 

 changing logo layout
 

 changing logo settings
 

 Rename vignettes menu to Guides and tidy navbar
 

 limps 1.3.6
- Change the terminology from "peptides" to "precursors" for the default input feature throughout the package.
- More discussion of precursors vs peptides and other levels of data in the vignette.
- Further clarification of the different levels of data that limpa can process.
- The output column `genes$NPeptides` from dpcQuant() renamed to `genes$NPrec`.
- Progress message from dpcQuant() and dpcQuantByRows() now uses "Precursors" instead of "Peptides" for number of rows.
- Percentage progress has been added.
- New argument `verbose` for readDIANN(). If `TRUE`, now gives message about number of filtered q-values.
- Bug fix to readDIANN() to avoid unnecessary message about `q.cutoffs` not being the correct length, when it is actually of length 1.
- Other code streamlining for readDIANN() and readSpectonaut().
 

 chore: Fix assignment note
 

 devel version bump
 

 version bump
 

 Vignette def updated
 

 Running ML example added
 

 output fixed
 

 docs added
 

 fixed mzqc converter
 

 Replace defunct arrange_() with arrange()
 

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

 Fix Rd warnings - bump to v1.3.3
 

 fix dups

Merge remote-tracking branch 'origin/main' into devel

# Conflicts:
#	man/group1_sampleData_sce.Rd
 

 Update README.md 

 fix rd names.
 

 Deprecated

 maintainer requested at bioc-devel
 

 Bugfix: improve genes' plot (#131)

* Improved readability of the 'genes' plot from cleanPlots()

* Improved genes' plot

The genes plot that is part of the `cleanPlots()` now uses
log-scale and shows the top 20 genes with `reppel`

* Fixed broken link to vignette in README.md

* Fixed typo

* Fixed type in NEWS.md 

 Fix vignette link in README

Updated the vignette link for COTAN v2 examples and corrected formatting. 

 Improvements for plot functions (#130)

* Fixed genes' plot in `cleanPlots()` and added `genesPercentagePlot()`

* Restored col name in df

Fixed possible issue with unevaluated cell in vignette 

 bump to 1.29.5
 

 tests: fix unit tests
 

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

 fix(patientRisk): ensure extended list expands gene selection
 

 Merge pull request #25 from rformassspectrometry/jomain

Replace msdata with MsDataHub 

 Merge pull request #377 from rformassspectrometry/jomain

refactor: replace msdata with MsDataHub 

 Increased max read no in all samples to 0x7ff0_0000
 

 bumps version
 

 SummarizedExperiment 1.41.1: Add missing exports combineRows and combineCols
 

 update documentation to reflect hiding supporting functions for enrichmentSets
 

 shorten line for bioc styling
 

 update project name in .Rbuildignore
 

 error handling in plotEnrich
 

 use ggtree for plotEnrich and reformatting for bioconductor
 

 update bioconductor version
 

 troubleshooting windows build failure
 

 remove Rsamtools dependency
 

 re-add figures
 

 rename vignette
 

 remove SEMplScores validity function
 

 suggest BiocStyle
 

 add the @source of SEMC
 

 add enrichmentSets to vignette
 

 update NEWS
 

 add functions for generating enrichment sets
 

 bump subminor
 

 Merge pull request #61 from Nanostring-Biostats/SeuratUpdate

Seurat slot deprecation 

 Merge branch 'master' of https://github.com/Nanostring-Biostats/SpatialDecon into SeuratUpdate
 

 Update to Bruker signature 

 Update auto-email 

 some fix
 

 Reuse some roxygen across h5createDataset() and h5createAttribute()
 

 Document H5type change in NEWS
 

 Add FIXME about using .setDataType()
 

 Add NEWS note about #68
 

 Use testthat for mocking
 

 Run desc::desc_normalize()
 

 Merge pull request #37 from rformassspectrometry/jomain

Replace msdata by MsDataHub 

 refactor: replace msdata by MsDataHub

- Use *MsDataHub* instead of *msdata*.
 

 refactor: replace msdata by MsDataHub

- Load test data from the *MsDataHub* package removing the dependency on
  the *msdata* package.
 

 refactor: update as per lintr
 

 test: fix unit tests
 

 chore: appease lintr
 

 chore: bump version and update NEWS.md
 

 doc: reoxygenate
 

 fixed the unit test and version update
 

 rename .url_location to .CBIOPORTAL_DATA_URL
 

 use stop in error
 

 version bump 2.51.1
 

 add extra level in unit test
 

 version fixed
 

 styling changes
 

 Version bump for ML functions
 

 removed dublicates
 

 MSstatsQC-ML functions added
 

 Deprecated
 

 fix test_that issue
 

 Bump version
 

 Add new function ConstructDNAMPanel
 

 Bug fix
 

 fixed a bug in soft clipping code
 

 added softclipping for cellCounts when detecteJunction is enabled.
 

 Merge pull request #76 from Chloriiin/feature/beta-smoother-tm-centering

Add documentations 

 Merge pull request #75 from Chloriiin/feature/beta-smoother-tm-centering

Feature/beta smoother tm centering 

 fix bugs from vignettes; fix version numbering per bioconductor rules
 

 Update DESCRIPTION 

 Updated version, wordlist, and corrected line length in vignette
 

 Bump version to 0.99.4 to trigger build and Fix BiocCheck: runnable examples, R version, DESCRIPTION
 

 update spliceSites<-() test for changes in TP53 annotation
 

 use the new concordant_uniq.bam from LungCancerLines to fix test
 

 add a new BAM file that is compatible with the current TP53 annotation
 

 successfully integrate ExperimentHub data loading and metadata
 

 Deprecated
 

 Deprecation
unresponsive
 

 Use SeuratObject layer= for counts extraction
 

 Deprecation
 

 Deprecation
unresponsive
 

 a possible fix for #96
 

 bugfree version
 

 Fix LaTeX errors: replace Unicode Greek letters with ASCII (v0.99.4)

Replace α/β with alpha/beta and × with * in applyBiologicalNoise.Rd
to fix LaTeX PDF generation errors in R CMD check.

https://claude.ai/code/session_015bgoj2L5THkuEG1Qu7w5xf
 

 Attempt to fix git issue with double filename plotstarlegend
 

 Merge pull request #11 from gbucci/claude/review-bioc-contribution-8DFCD

Refactor seed handling: use set.seed() instead of function parameter 

 Reconciling joss
 

 Reconciling joss
 

 Update DESCRIPTION 

 Update README.md 

 Review 1 implementation 

 Create imgB 

 Review 1 update of paper.md 

 Deleted workflows 

 Update draft-pdf.yml 

 Update draft-pdf.yml 

 Updated subfolder for joss submission 

 Named joss folder appropriately 

 Merge pull request #10 from gbucci/claude/fix-bioconductor-errors-bgw5b

## Bioconductor Build Fixes (v0.99.2)

Addresses all ERROR and WARNING issues from Bioconductor build system.

### ✅ Errors Fixed:
- **LaTeX Unicode errors**: Replaced Greek characters (α, β) with ASCII (alpha, beta)
- **set.seed() in package code**: Removed completely from simulateTumor() function
- **Documentation warnings**: Removed obsolete man/accessors.Rd file

### 📋 Changes:
- `DESCRIPTION`: Version 0.99.1 → 0.99.2
- `R/noise_model.R`: ASCII characters in documentation
- `R/simulateTumor.R`: Removed seed parameter completely
- `man/simulateTumor.Rd`: Updated documentation
- `tests/`: All test files updated to use set.seed() before function calls
- `man/accessors.Rd`: Removed (obsolete file)
 

 # sfi 0.99.3

* Renamed `getqc()` to `get_sfi_params()` to better reflect its purpose. It now returns a named vector `c(window, idelta)` instead of an unnamed vector.
* Renamed `getqcdf()` to `get_qc_features()` for clarity.
* `getmzml()` now returns a `data.frame` with named columns (`mz`, `intensity`, `rt`) instead of a matrix.
* `getsfm()` (Sample Feature Matrix) and `get_qc_features()` now set informative row names corresponding to the sample injection index.
* Expanded vignette with "Using the Results" and "Downstream Analysis" sections, demonstrating integration with `SummarizedExperiment`.
* Detailed documentation for return values and column definitions for `getsfm`, `getsff`, and `get_qc_features`.
* Updated README installation instructions for Bioconductor.
* Added a comprehensive `testthat` test suite.
* Updated `DESCRIPTION` to set `LazyData: false` per Bioconductor guidelines.
* Added `SummarizedExperiment` to `Suggests`.
* Updated `find_2d_peaks` to return an object with class c("sfi_peaks", "data.frame"). All the related functions have been updated.
 

 Delete paper/temp.text 

 Reconcile README.md 

 Merge branch 'devel'

JOSS pubblication update
 

 Review 1 update of paper.md

JOSS publication incorporated
 

 Deleted workflows 

 Update draft-pdf.yml 

 Update draft-pdf.yml 

 Updated subfolder for joss submission

JOSS publication update
 

 Named joss folder appropriately

JOSS review update
 

 Update draft.yml 

 Create draft.yml 

 Update NEWS 

 Review 1 implementation 

 Delete vignettes/exData/imgB 

 Review 1 update of readme.txt 

 Update paper.md 

 Update draft-pdf.yml 

 Update draft-pdf.yml 

 Create draft-pdf.yml 

 Update README.md 

 Created a subfolder for joss submission 

 Update README.md for JOSS submission 

 Create CONTRIBUTING.md 

 Update paper.md 

 Delete vignettes/FIG1.png 

 Create draft-pdf.yml 

 Delete .github/workflows/draft.yml 

 Update paper.bib 

 Update draft-pdf.yml 

 Delete vignettes/.github directory 

 Delete vignettes/.github/workflows directory 

 Create draft-pdf.yml 

 Delete vignettes/workflows directory 

 Pasted full license statement 

 Updated abbreviations in bibliography 

 FIG0 revised 

 JOSS article first draft 

 Update DESCRIPTION 

 Update README.md 

 Review 1 implementation 

 Create imgB 

 Review 1 update of paper.md 

 Deleted workflows 

 Update draft-pdf.yml 

 Update draft-pdf.yml 

 Updated subfolder for joss submission 

 Named joss folder appropriately 

 Update draft.yml 

 Create draft.yml 

 Update README.md for JOSS submission 

 Create CONTRIBUTING.md 

 Update paper.md 

 Delete vignettes/FIG1.png 

 Create draft-pdf.yml 

 Delete .github/workflows/draft.yml 

 Update paper.bib 

 Update draft-pdf.yml 

 Delete vignettes/.github directory 

 Delete vignettes/.github/workflows directory 

 Create draft-pdf.yml 

 Delete vignettes/workflows directory 

 Pasted full license statement 

 Updated abbreviations in bibliography 

 FIG0 revised 

 JOSS article first draft 

 Merge pull request #9 from gbucci/claude/update-clonalsim-r-requirement-bgw5b

Update to v0.99.1 - Fix R requirement and seed parameter for Bioconductor 

 Fix R version requirement and seed parameter

Fix documentation: update seed parameter default from 123 to NULL 

 Merge pull request #7 from gbucci/claude/update-clonalsim-r-requirement-bgw5b

Claude/update clonalsim r requirement bgw5b 

 Merge pull request #6 from gbucci/main

merge 

 Fix 'object seed not found' error in simulateTumor()

The function was referencing an undefined 'seed' variable in the
metadata section. Now properly captures the current .Random.seed
from the global environment if it exists, otherwise sets it to NULL.
This preserves reproducibility when users set a seed with set.seed()
before calling simulateTumor().
 

 Update R version requirement from 4.6.0 to 4.4.0

R 4.6.0 is not yet available on CRAN. The latest stable version
is 4.5.2. Updated the minimum R version requirement to 4.4.0 to
ensure compatibility with currently available R versions.
 

 Fix Bioconductor build errors and warnings

Address all critical issues identified in the Bioconductor build report:

ERRORS fixed:
- Remove ClonalSim.Rproj from repository (system file)
- Remove fishplot from Suggests (not available in official repos)
- Remove inst/CITATION file (no DOI available yet)

WARNINGS fixed:
- Remove empty inst/scripts directory and its contents
- Remove set.seed() calls from package code
- Add proper documentation to accessor functions

Other improvements:
- Update R dependency to >= 4.6.0 as recommended
- Remove devtools from Suggests (not needed)
- Add note about set.seed() in simulateTumor documentation

The package should now pass BiocCheck without errors or warnings.
 

 add deprecation startup message
 

 Merge pull request #139 from jessmcc22/devel

Updated Vignette to reflect AIC changes 

 Spelling correction
 

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

 Merge pull request #138 from jessmcc22/devel

Added boxplot, aic_median, and non-discrete data option for AIC; also added advanced features check box for Harman correction 

 Updated compute_aic to include a boxplot, aic_median value, and to run for nondiscrete data
 

 Update AIC method to allow non-discrete data for lognormal and voom comparison.
 

 lintr
 

 update version number
 

 added harman correction to shiny
fixed shiny bugs