Changes in version 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.

                 Changes in version 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.

                 Changes in version 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.

                 Changes in version 1.22.1 (2024-10-29)                 

  - Fixed issue with enrichR not being loaded

                 Changes in version 1.22.0 (2024-10-29)                 

  - Update to match Bioconductor release version

                 Changes in version 1.18.2 (2024-04-02)                 

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

                 Changes in version 1.18.1 (2023-11-05)                 

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

                 Changes in version 1.14.2 (2023-01-19)                 

  - Update to match Bioconductor release version

                 Changes in version 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

                 Changes in version 1.12.0 (2022-04-30)                 

  - Update to match Bioconductor 3.15 release version

                 Changes in version 1.11.1 (2022-03-31)                 

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

                 Changes in version 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

                 Changes in version 1.10.0 (2021-12-28)                 

  - Update to match Bioconductor release version

                 Changes in version 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

                 Changes in version 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.

                 Changes in version 1.7.7 (2021-04-12)                  

  - Added handling for sparse matrices

                 Changes in version 1.7.6 (2021-04-04)                  

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

                 Changes in version 1.7.4 (2021-03-09)                  

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

                 Changes in version 1.1.6 (2019-07-16)                  

  - Add multiclass decision tree

                 Changes in version 1.1.4 (2019-05-28)                  

  - Add Alternate headings support for plotDimReduceFeature

                 Changes in version 1.1.3 (2019-05-14)                  

  - Add multiclass decision tree (MCDT) cell cluster annotation

                 Changes in version 1.1.2 (2019-05-14)                  

  - Fix a bug in celdaHeatmap

                 Changes in version 1.0.1 (2019-05-09)                  

  - Default seed setting to maintain reproducibility

                Changes in version 0.99.34 (2019-04-23)                 

  - Minor changes to the vignettes

                Changes in version 0.99.23 (2019-04-10)                 

  - Remove pheatmap import

                Changes in version 0.99.22 (2019-04-09)                 

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

                 Changes in version 0.99.8 (2019-03-11)                 

  - Second submission to Bioconductor

                 Changes in version 0.99.0 (2018-05-15)                 

  - First submission to Bioconductor