fgsea: Fast Gene Set Enrichment Analysis

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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 <alsergbox@gmail.com>
License
MIT + file LICENCE
Version
1.0.2
URLs

View on Bioconductor

Man pages

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

Files in this package

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