NEWS.md

In ncborcherding/escape: Easy single cell analysis platform for enrichment

escape VERSION 2.2.2

UNDERLYING CHANGES

• fix performNormalization() conditional statements
• fix performNormalization() rescaling for per gene set calculations

escape VERSION 2.2.1

VERSION BUMP FOR BIOCONDUCTOR

escape VERSION 2.1.5 (2024-10-23)

• update handling of v5 Seurat versus <v5 Seurat Objects
• added mean and median visualization for heatmapEnrichment()

escape VERSION 2.1.4 (2024-09-13)

• update densityEnrichment() GSVA function pull

escape VERSION 2.1.3 (2024-09-13)

VERSION BUMP FOR BIOCONDUCTOR

UNDERLYING CHANGES

• update densityEnrichment() for new GSVA function name
• Parallelization of performNormalization()
• Refactor of getGeneSets() to prevent issues with m_df error.

escape VERSION 2.0.1 (2024-07-26)

UNDERLYING CHANGES

• fixed performNormalziation() errors when input.data was a matrix, now requires single-cell object and enrichment data
• passing parallel processing properly to runEscape() function.

escape VERSION 1.99.1 (2024-02-29)

UNDERLYING CHANGES

• ordering by mean values no longer changes the color order
• add explicit BPPARAM argument to runEscape() and escape.matrix()
• added additional details in runEscape() and escape.matrix() for make.positive.
• removed plotting of splitEnrichment() for group.by = NULL
• separated AUC calculation to rankings and AUC, this was only method found to get consistent scores.

escape VERSION 1.99.0 (2024-02-27)

NEW FEATURES

• Added runEscape()
• Added geyserEnrichment()
• Added scatterEnrichment()
• Added heatmapEnrichment()
• Changed enrichIt to escape.matrix()
• Changed enrichmentPlot to densityEnrichment()
• performPCA() now works with a matrix or single-cell object
• pcaEnrichment() combines biplot-like functions

UNDERLYING CHANGES

• Updated interaction with gsva package
• Added support for GSVA calculation
• Added support for AUCell calculation
• Added support of visualizations and calculations for single-cell objects
• Modified getGeneSets() to output a list of gene set objects with reformatted names following the Seurat "-" convention

DEPRECATED AND DEFUNCT

• Deprecate getSignificance()
• Deprecate masterPCAPlot()

CHANGES IN VERSION 1.9.0

• Releveling version for commit to new Bioconductor release
• Removed UCell internal functions to just import the Bioconductor UCell package

CHANGES IN VERSION 1.4.2

• Fixed masterPCAPlot top_n() call to slice_max by top.contributions.

CHANGES IN VERSION 1.4.1

• Version number and small edits for bioconductor compliance
• Removed singscore method
• Added UCell functions internally so they are compatible with Bioconductor
• Fixed performPCA, eliminated merge call.

CHANGES IN VERSION 1.3.4

• Normalization for ssGSEA no longer uses the range of all gene sets, but columns, normalizing it to 0 to 1.
• Added Kruskal-Wallis test for additional support of multi-group comparison

CHANGES IN VERSION 1.3.3

• Added wilcoxon and LR for getSignificance
• median calculated and appended to the getSignificance() function output
• ANOVA in getSignificance() returns p-values for each comparison using TukeyHSD()
• new parameter gene.sets getSignificance() to select only gene sets or subsets.
• enrichmentPlot() beta release
• Added subcategory to getGeneSets to select subsets of libraries.
• Added default coloring to enrichmentPlot()
• enrichmentPlot() now imports calculations partially from GSVA internal functions to facilitate use of C
• Filtering based on min.size now works instead of not working.

CHANGES IN VERSION 1.3.2

• Added removal of gene sets with less than x features parameter in enrichIt - min.size
• Added UCell and singScore support
• new parameter gene.sets in MasterPCAPlot() and performPCA() to allow for selecting specific columns and prevent using other numeric vectors in meta data.

CHANGES IN VERSION 1.3.1

• Aligning versions to the current bioconductor release
• Added DietSeurat() call in vignette to prevent issues
• Adding internal gene sets - escape.gene.sets
• Removed lm.fit using limma from getSignificance

CHANGES IN VERSION 1.0.1

• Removed ggrepel, rlang, and factoextra dependencies.
• Updated Seurat package switch
• Switch the way counts are processed by first eliminating rows with 0 expression in the sparse matrix before converting to a full matrix

CHANGES IN VERSION 0.99.9

• Changing Seurat dependency, updated vignette

CHANGES IN VERSION 0.99.8

• Edited getSignificance ANOVA model call

CHANGES IN VERSION 0.99.7

• Edited getSignificance fit call to match documentation

CHANGES IN VERSION 0.99.6

• Edited match.args() in getSignificance

CHANGES IN VERSION 0.99.5

• Edited match.args() in getSignificance

CHANGES IN VERSION 0.99.4

• Added match.args() to getSignificance
• Changed stop() to message()
• Modified getSignficance to allow for ANOVA and T.test

CHANGES IN VERSION 0.99.3

• Updated link in description of getGeneSets.

CHANGES IN VERSION 0.99.2

*Fixed a parenthesis, yeah a parenthesis. (In enrichIt() call I edited for 99.1)

CHANGES IN VERSION 0.99.1

• Removed parallel call in gsva() and added biocparallel
• Changed cores = 4 to cores = 2 in the vignette

CHANGES IN VERSION 0.99.0

• Preparing for bioconductor submission

ncborcherding/escape documentation built on Dec. 1, 2024, 8:12 a.m.