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
 

 Merge pull request #136 from jessmcc22/devel

Updated AIC to provide AIC metric 

 Merge pull request #134 from hjfan527/devel

Added color to kBET plot 

 Merge branch 'wejlab:devel' into devel
 

 Added color to kBET plot
 

 spelling corrections
 

 Updated thresholds, added p_value helper function, updated commentary
 

 Merge pull request #132 from jessmcc22/devel

Update negative binomial to allow user choice for small sample size and place holders for edgeR implementation 

 Updated Version
 

 Increased umap point size
 

 Merge pull request #131 from jessmcc22/devel

Various Updates: updated lambda stat to provide statistic even for unbalanced designs; Added log_option to UMAP and updated example in BatchQC_Intro vignette, including utilizing PCA log option; removed redundantt "Warning" label in kBET warning; removed as.numeric and changed to is.numeric in dendrogram_alpha_numeric_check 

 removed redundnat "Warning" label in warning
 

 Added log_option to UMAP and updated example in BatchQC_Intro vignette; also updated PCA example to utilize the log feature
 

 updated lambda stat to provide statistic even for unbalanced designs
 

 Merge pull request #57 from shbrief/RELEASE_3_22

fix the build error by updating the rols function names 

 update the name of exported functions from rols package
 

 gitignoer
 

 Merge pull request #113 from gdrplatform/GDR-2854

Gdr 2854 

 chore: appease lintr
 

 chore: bump version and update changelog
 

 version 1.1.5 bump
 

 adding polygonsCol to cosmx
 

 cleaning LICENSE note
 

 Version bump
 

  DESCRIPTION file to update changes
 

 Package info and vignette update
 

 Changed default token_url to internal constant
 

 Updated package info
 

 Refactored new_submission workflow
 

 Added possibility to use OS credential storage for passwords
 

 Test linting
 

 Package info update
 

 Added text length validations to analyses
 

 Updated excel template
 

 Update comments, API operation names
 

 Edit README.md 

 Updated package info
 

 Added tests for new functions
 

 Added validation functions and argument validation
 

 Updated formatting
 

 Added function argument validation
 

 Rd and namespace update
 

 Added validation of title and description lengths
 

 Bump version to 1.3.5 for Bioc devel
 

 version bump to devel.
 

 one last thing to resolve
 

 Update NEWS re test changes and argument change as of Jan/Feb 2026
 

 Clear MIT licence info as it was giving an error.
 

 Size argument in geom_rect() is depreciated so needs to be replaced with linewidth.
 

 New ggplot object S7 rather than S3 as per version 4.0.0 of ggplot2.
Required changes to lots of tests.
 

 Merge pull request #36 from brennanpincardiff/change_tests

update documentation to avoid a warning. 

 Merge pull request #35 from brennanpincardiff/change_tests

Need to change length of object due to changes in ggplot2 3.5.0 

 Merge pull request #31 from stevin-wilson/master

Adding transparency option to the draw* functions 

 added transparency parameter into the documentation
 

 Merge pull request #25 from brennanpincardiff/RELEASE_3_11

Release 3 11 

 Merge pull request #23 from brennanpincardiff/master

Improvement to function extract_feat_acc 

 Bumped version 1.6.1
 

 Bumped version number
 

 Add option to select terms for regROTS
 

 added mm39 tracks
 

 fix: interpret() empty result and optimize prompt for NK cell annotation
 

 new sticker
 

 feat: implement gene-based fallback mode for interpret function

- Update 'process_enrichment_input' to extract raw gene lists from input objects
- Modify 'interpret' and 'interpret_agent' to handle cases with no enriched pathways
- Add 'fallback_mode' to agent prompts to guide conservative interpretation
- Update NEWS.md and create fallback-mode-article.md
- Refine SCI_Paper_Plan.md with enhanced methodology and case studies
 

 feat: enhance interpret functionality with visualization and refactoring

- Refactor 'interpret.R' to extract PPI logic into helper function '.get_ppi_context_text'
- Improve robustness in 'run_agent_synthesizer' with null checks
- Implement 'plot.interpretation' method using 'ggtangle' for network visualization
- Update DESCRIPTION to suggest 'ggtangle'
- Update NEWS.md with new features
 

 feat: introduce Knowledge-Guided Interpretation (PPI, Hub Genes, Fold Change, and Causal Integration)