The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.
|Author||Alexey Sergushichev [aut, cre]|
|Date of publication||None|
|Maintainer||Alexey Sergushichev <email@example.com>|
|License||MIT + file LICENCE|
calcGseaStat: Calculates GSEA statistics for a given query gene set
calcGseaStatCumulative: Calculates GSEA statistic values for all the prefixes of a...
examplePathways: Example list of mouse Reactome pathways.
exampleRanks: Example vector of gene-level statistics obtained for Th1...
fgsea: Runs preranked gene set enrichment analysis.
gmtPathways: Returns a list of pathways from a GMT file.
plotEnrichment: Plots GSEA enrichment plot.
plotGseaTable: Plots table of enrichment graphs using ggplot and gridExtra.
reactomePathways: Returns a list of Reactome pathways for given Entrez gene IDs