NEWS

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celda 1.29.3 (2026-10-09)

• The decontX vignette is now a short pointer to the decontX package's vignette, which has the full, maintained DecontX tutorial; celda no longer keeps its own copy. The duplicate pkgdown article (decontX_pbmc4k) was removed, and the site's DecontX menu entry now links to the decontX vignette on Bioconductor.

celda 1.29.2 (2026-10-09)

• Fixed the decontX vignette, which failed to build on Bioconductor devel with "'groupClusters' not found in 'z': 6". It hard-coded cluster numbers from decontX's heuristic clustering, which differ between decontX versions and platforms. The vignette now maps each cell type to the cluster where its marker genes are detected most often, as the decontX package's own vignette does.

celda 1.29.1 (2026-09-25)

• Replaced deprecated ggplot2::aes_string() (and size for line geoms) with tidy-eval aes() / linewidth in the dimension-reduction, violin, and perplexity plotting functions, silencing ggplot2 deprecation warnings (#418).
• Migrated the DecontX implementation to the standalone decontX Bioconductor package. celda's decontX(), decontXcounts(), plotDecontXContamination(), plotDecontXMarkerExpression(), plotDecontXMarkerPercentage(), and simulateContamination() are now thin, backward-compatible wrappers around the decontX package (added to Suggests).
• Removed celda's DecontX C++ backend (src/DecontX.cpp) and dropped the DecontX-only dependencies MCMCprecision, scater, scran, and DelayedArray from Imports (scater retained in Suggests for the vignettes).
• Bioconductor release readiness: replaced T/F logical literals with TRUE/FALSE in findMarkersTree.R (BiocCheck WARNING); added a URL field and bumped the R dependency to R (>= 4.6.0) in DESCRIPTION; set LazyData: false; added labels to unlabeled vignette knitr chunks; and added the required url field to _pkgdown.yml.
• Declared Seurat in Suggests and namespaced the Seurat::Idents() and Seurat::RunUMAP() calls in findMarkersTree()'s Seurat-object input path, clearing the remaining R CMD check "no visible global function" NOTE.

celda 1.22.1 (2024-10-29)

• Fixed issue with enrichR not being loaded

celda 1.22.0 (2024-10-29)

• Update to match Bioconductor release version

celda 1.18.2 (2024-04-02)

• Updated Makevar files to new CRAN standards
• Fixed unit test causing error

celda 1.18.1 (2023-11-05)

• Update to match Bioconductor release version
• Removed multipanelfigure as a dependency

celda 1.14.2 (2023-01-19)

• Update to match Bioconductor release version

celda 1.13.0 (2022-10-20)

• Bug fixes related to cluster labels stored as factors and plotting
• Updated sparse matrix conversion to work with Matrix v1.4-2

celda 1.12.0 (2022-04-30)

• Update to match Bioconductor 3.15 release version

celda 1.11.1 (2022-03-31)

• Fixes to reports
• Use smoothe splines for perplexity and RPC plots

celda 1.11.0 (2022-03-31)

• Improvments to decontX vignette
• Added ability to subsample to speed up perplexity calculations
• Added ability to use batch parameter with the raw matrix in decontX

celda 1.10.0 (2021-12-28)

• Update to match Bioconductor release version

celda 1.9.3 (2021-10-04)

• Fixed bug in checking background matrix with decontX
• Switched to using Github Actions for Continuous Integration
• Fixed plotting bugs in celda results reports
• Speed up final step in decontX when creating final decontaminated matrix

celda 1.9.2 (2021-07-19)

• Added a NEWS.md file to track changes to the package.
• Added new tutorials and documentation generated with pkgdown.
• Removed warnings in plotRPC functions.
• Added use of "displayName" to several functions that show feature names.
• Minor bug fix when the input matrix was sparse and contained non-integer values.
• Several improvements to plotting functions.

celda 1.7.7 (2021-04-12)

• Added handling for sparse matrices

celda 1.7.6 (2021-04-04)

• Added functions for creating HTML reports
• Fixed bug in decontX plotting

celda 1.7.4 (2021-03-09)

• Enable input of raw/droplet matrix into decontX to estimate ambient RNA

celda 1.1.6 (2019-07-16)

• Add multiclass decision tree

celda 1.1.4 (2019-05-28)

• Add Alternate headings support for plotDimReduceFeature

celda 1.1.3 (2019-05-14)

• Add multiclass decision tree (MCDT) cell cluster annotation

celda 1.1.2 (2019-05-14)

• Fix a bug in celdaHeatmap

celda 1.0.1 (2019-05-09)

• Default seed setting to maintain reproducibility

celda 0.99.34 (2019-04-23)

• Minor changes to the vignettes

celda 0.99.23 (2019-04-10)

• Remove pheatmap import

celda 0.99.22 (2019-04-09)

• Package celda, for bi-clustering of single-cell 'omics data.

celda 0.99.8 (2019-03-11)

• Second submission to Bioconductor

celda 0.99.0 (2018-05-15)

• First submission to Bioconductor