sigPathway: Pathway Analysis

Conducts pathway analysis by calculating the NT_k and NE_k statistics as described in Tian et al. (2005)

AuthorWeil Lai (optimized R and C code), Lu Tian and Peter Park (algorithm development and initial R code)
Date of publicationNone
MaintainerWeil Lai <wlai@alum.mit.edu>
LicenseGPL-2
Version1.42.0
http://www.pnas.org/cgi/doi/10.1073/pnas.0506577102, http://www.chip.org/~ppark/Supplements/PNAS05.html

View on Bioconductor

Functions

calcTNullFast Man page
calcTStatFast Man page
calculate.GSEA Man page
calculate.NEk Man page
calculate.NGSk Man page
calculate.NTk Man page
estimateNumPerm Man page
G Man page
getPathwayStatistics Man page
getPathwayStatistics.NGSk Man page
gmtToG Man page
gmxToG Man page
grpToG Man page
importGeneSets Man page
MuscleExample Man page
phenotype Man page
rankPathways Man page
rankPathways.NGSk Man page
runSigPathway Man page
selectGeneSets Man page
tab Man page
writeSigPathway Man page
writeSP Man page
xmlToG Man page

Files

sigPathway/CHANGELOG
sigPathway/DESCRIPTION
sigPathway/NAMESPACE
sigPathway/R
sigPathway/R/calcGeneSetStat.R sigPathway/R/calcProbeStat.R sigPathway/R/checkInputs.R sigPathway/R/estimateNumPerm.R sigPathway/R/getPathwayStat.R sigPathway/R/importGeneSets.R sigPathway/R/rankPathways.R sigPathway/R/runSigPathway.R sigPathway/R/selectGeneSets.R sigPathway/R/writeHTML.R
sigPathway/build
sigPathway/build/vignette.rds
sigPathway/data
sigPathway/data/MuscleExample.RData
sigPathway/inst
sigPathway/inst/doc
sigPathway/inst/doc/sigPathway-vignette.R
sigPathway/inst/doc/sigPathway-vignette.Rnw
sigPathway/inst/doc/sigPathway-vignette.pdf
sigPathway/man
sigPathway/man/MuscleExample.Rd sigPathway/man/calcTNullFast.Rd sigPathway/man/calcTStatFast.Rd sigPathway/man/calculate.GSEA.Rd sigPathway/man/calculate.NGSk.Rd sigPathway/man/calculatePathwayStatistics.Rd sigPathway/man/estimateNumPerm.Rd sigPathway/man/getPathwayStatistics.NGSk.Rd sigPathway/man/getPathwayStatistics.Rd sigPathway/man/importGeneSets.Rd sigPathway/man/rankPathways.NGSk.Rd sigPathway/man/rankPathways.Rd sigPathway/man/runSigPathway.Rd sigPathway/man/selectGeneSets.Rd sigPathway/man/writeSigPathway.Rd
sigPathway/src
sigPathway/src/Makevars
sigPathway/src/calc_gene_set_internal.c
sigPathway/src/calc_gene_set_stat.c
sigPathway/src/calc_probe_stat.c
sigPathway/src/calc_weights.c
sigPathway/src/matrix_fn.c
sigPathway/src/permute.c
sigPathway/src/shuffle.c
sigPathway/src/sigPathway.c
sigPathway/src/sigPathway.h
sigPathway/vignettes
sigPathway/vignettes/MHC1.png
sigPathway/vignettes/TopPathwaysTable.png
sigPathway/vignettes/sigPathway-vignette.Rnw
sigPathway/vignettes/sigPathway-vignette.bib

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