PGSEA: Parametric Gene Set Enrichment Analysis

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Parametric Analysis of Gene Set Enrichment

Author
Kyle Furge <kyle.furge@vai.org> and Karl Dykema <karl.dykema@vai.org>
Date of publication
None
Maintainer
Karl Dykema <karl.dykema@vai.org>
License
GPL-2
Version
1.48.0

View on Bioconductor

Man pages

aggregateExprs
Aggregate expression data
convertSmc
Convert Entrez ID based "smc" object
editSmc
Edit "smc" objects
go2smc
Gene Ontology 2 "smc"
GOLUBmcs
Molecular Concepts prepared at VAI from data created by Golub...
kegg2smc
KEGG pathway to "smc"
nbEset
Reduced Neuroblastoma data set
PGSEA
Parametric Gene Set Enrichment Analysis
readGmt
readGmt
readSmc
Read SMC files
scanSmc
Scan through smc objects
smcPlot
Plot PGSEA results
VAIgsc
Molecular Concepts (Gene Sets) prepared at VAI
VAImcs
Molecular Concepts prepared at VAI
writeGmt
writeGmt
writeSmc
writeSmc

Files in this package

PGSEA/DESCRIPTION
PGSEA/NAMESPACE
PGSEA/R
PGSEA/R/PGSEA.R
PGSEA/build
PGSEA/build/vignette.rds
PGSEA/data
PGSEA/data/GOLUBmcs.rda
PGSEA/data/VAIgsc.rda
PGSEA/data/VAImcs.rda
PGSEA/data/nbEset.rda
PGSEA/inst
PGSEA/inst/doc
PGSEA/inst/doc/PGSEA.R
PGSEA/inst/doc/PGSEA.Rnw
PGSEA/inst/doc/PGSEA.pdf
PGSEA/inst/doc/PGSEA2.R
PGSEA/inst/doc/PGSEA2.Rnw
PGSEA/inst/doc/PGSEA2.pdf
PGSEA/inst/extdata
PGSEA/inst/extdata/sample.gmt
PGSEA/man
PGSEA/man/GOLUBmcs.Rd
PGSEA/man/PGSEA.Rd
PGSEA/man/VAIgsc.Rd
PGSEA/man/VAImcs.Rd
PGSEA/man/aggregateExprs.Rd
PGSEA/man/convertSmc.Rd
PGSEA/man/editSmc.Rd
PGSEA/man/go2smc.Rd
PGSEA/man/kegg2smc.Rd
PGSEA/man/nbEset.Rd
PGSEA/man/readGmt.Rd
PGSEA/man/readSmc.Rd
PGSEA/man/scanSmc.Rd
PGSEA/man/smcPlot.Rd
PGSEA/man/writeGmt.Rd
PGSEA/man/writeSmc.Rd
PGSEA/vignettes
PGSEA/vignettes/PGSEA.Rnw
PGSEA/vignettes/PGSEA2.Rnw