NEWS.md

In montilab/hypeR: An R Package For Geneset Enrichment Workflows

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

• Published in Bioinformatics
• https://doi.org/10.1093/bioinformatics/btz700

montilab/hypeR documentation built on Oct. 29, 2023, 12:01 p.m.