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

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Files in this package

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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