Celda Release v1.18.1

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

Celda Release v1.14.2

This release contains updates from two versions:

celda v1.14.2 (2023-01-19)

• Update to match Bioconductor release version

celda v1.13.0 (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 Release v1.12.0

This release contains updates from three versions:

celda v1.12.0 (2022-04-30)

• Update to match Bioconductor 3.15 release version

celda v1.11.1 (2022-03-31)

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

celda v1.11.0 (2022-03-31)

• Improvements 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 Release v1.10.0

• Update version number to match Bioconductor release

Celda Release v1.9.3

• 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 Release v1.9.2

• 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 Release v1.7.3

This version contains source codes used in Celda manuscript.

Celda Release v1.5.11

The initial release that passed Bioconductor development build check system without error or warnings. Some notable changes compared to the current stable release version on Bioconductor:

• Most functions in Celda can now take SingleCellExperiment object as input and output.
• moduleHeatmap and celdaProbabilityMap functions now use ComplexHeatmap::Heatmap to plot heatmaps.
• Other usage improvements including addition of new functions (selectFeatures, plotGridSearchPerplexityDiff, splitModule) and documentation updates.

The purpose of switching to SingleCellExperiment object is to incorporate count matrices, variable feature count matrices, Celda results, and column and row annotations into one overarching object. SingleCellExperiment object fits well for this task.

decontX_paper

This release contains the version of decontX that was used in decontX paper.