fgsea: Fast Gene Set Enrichment Analysis
Version 1.2.1

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.

AuthorAlexey Sergushichev [aut, cre]
Bioconductor views DifferentialExpression GeneExpression GeneSetEnrichment Pathways
Date of publicationNone
MaintainerAlexey Sergushichev <alsergbox@gmail.com>
LicenseMIT + file LICENCE
Version1.2.1
URL https://github.com/ctlab/fgsea/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("fgsea")

Getting started

README.md
Using fgsea package

Popular man pages

calcGseaStat: Calculates GSEA statistics for a given query gene set
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.
See all...

All man pages Function index File listing

Man pages

calcGseaStat: Calculates GSEA statistics for a given query gene set
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

Functions

Files

DESCRIPTION
LICENCE
NAMESPACE
NEWS
R
R/RcppExports.R
R/fgsea-package.R
R/fgsea.R
R/pathways.R
R/plot.R
README.md
build
build/vignette.rds
data
data/examplePathways.rda
data/exampleRanks.rda
inst
inst/CITATION
inst/doc
inst/doc/fgsea-tutorial.R
inst/doc/fgsea-tutorial.Rmd
inst/doc/fgsea-tutorial.html
inst/extdata
inst/extdata/fgsea_res.tsv
inst/extdata/mouse.reactome.gmt
inst/extdata/naive.vs.th1.rnk
inst/gen_gene_ranks.R
inst/gene_reactome_pathways.R
inst/run_broad_gsea.R
inst/th1_gsea.R
man
man/calcGseaStat.Rd
man/examplePathways.Rd
man/exampleRanks.Rd
man/fgsea.Rd
man/gmtPathways.Rd
man/plotEnrichment.Rd
man/plotGseaTable.Rd
man/reactomePathways.Rd
src
src/RcppExports.cpp
src/fastGSEA.cpp
src/fastGSEA.h
src/fgsea_init.c
tests
tests/testthat
tests/testthat.R
tests/testthat/test_gsea_analysis.R
tests/testthat/test_gsea_stat.R
tests/testthat/test_pathways.R
tests/testthat/test_plot.R
vignettes
vignettes/fgsea-tutorial.Rmd
fgsea documentation built on May 20, 2017, 9:37 p.m.

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