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NEWS.md

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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