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NEWS.md

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hypeR 2.0.1

  • Dots plots are now explicitly sized with size_by=c("genesets", "significance", "none")

hypeR 2.0.0

  • Version bump for bioconductor

hypeR 1.9.1

  • msigdb_download() filters by distinct gene symbols within genesets (relevant to msigdb >=7.4.1)

hypeR 1.9.0

  • Version bump for bioconductor

hypeR 1.7.2

  • Add hyp_to_graph()
  • Add optional igraph export for hyp_hmap()
  • Switch hyp_hmap() node coloring codes from rgba to hex
  • Fix warning from deprecated guides() functionality

hypeR 1.7.1

  • Add additional input checks for rgsets objects
  • Automatic removal of self loops from rgsets edges

hypeR 1.7.0

  • Version bump for bioconductor

hypeR 1.5.3

  • rctbl_build() now wraps hyp objects into unlabled multihyp objects
  • rctbl_build() nested tables shows the number of enriched genesets

hypeR 1.5.2

  • Correct file extensions (.rmd/.html) from output of hyp_to_rmd()
  • Relative paths are now supported by hyp_to_rmd()

hypeR 1.5.1

  • Fixed bug for wrong column names from enrichr_available()
  • Added the first shiny module for geneset selection

hypeR 1.5.0

  • Version bump for bioconductor
  • Fixed hyp_dots(merge=TRUE) bug where some genesets were not showing
  • Added support for fetching non-human Enrichr libraries (e.g. Yeast, Fly, Worm, Fish)
  • Better reporting through rctbl_hyp() and rctbl_mhyp()

hypeR 1.4.0

  • Version bump for bioconductor

hypeR 1.3.1

  • Ability to clean genesets names
  • Multiple signatures can now be merged into a single plot with hyp_dots(merge=TRUE)
  • Set the hyp_dots() legend title to the significance measure used
  • Versioning information used in export functions now includes parameters passed to hypeR()

hypeR 1.3.0

  • Version bump for bioconductor

hypeR 1.2.0

  • Added the genesets object with versioning
  • Downloaded genesets are now wrapped into gsets or rgsets objects automatically
  • Added functionality to download genesets directly from enrichr
  • Simplified functionality to download genesets via msigdbr
  • Genesets versioning is included by default in exporting/reporting functions
  • Tables now include the size of signatures, genesets, and the background distribution
  • Converted lapply() functions to mapply()
  • Removed option to disable titles when multiple signatures are plotted
  • Removed option to show/return plots
  • Some variable names across functions were made shorter or more clear
  • Version bump for bioconductor

hypeR 1.1.10

  • Changed default order of elements under each tab in hyp_to_rmd() function

hypeR 1.1.9