GSReg: Gene Set Regulation (GS-Reg)
Version 1.10.0

A package for gene set analysis based on the variability of expressions as well as a method to detect Alternative Splicing Events . It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods. For detecting Differentially Spliced genes, it provides an implementation of the Spliced-EVA (SEVA).

Browse man pages Browse package API and functions Browse package files

AuthorBahman Afsari <bahman@jhu.edu>, Elana J. Fertig <ejfertig@jhmi.edu>
Bioconductor views AlternativeSplicing GeneExpression GeneRegulation GeneSetEnrichment GeneticVariability Pathways
Date of publicationNone
MaintainerBahman Afsari <bahman@jhu.edu>, Elana J. Fertig <ejfertig@jhmi.edu>
LicenseGPL-2
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GSReg")

Man pages

GSReg_GeneSets_DIRAC: Performs DIRAC for gene set analysis from the paper Eddy et...
GSReg_GeneSets_VReg.: Performs Gene Set Analysis using Expression Variation...
GSReg_Kendall: Calculate Kendall-tau distance in different forms
GSReg_OverlapJunction: Generates junction overlap matrices required for SEVA
GSReg-package: A package for Gene Set Analysis based on the variability of...
GSReg_SEVA: Applies Splice-EVA (SEVA) algorithm

Functions

GSReg Man page
GSReg-package Man page
GSReg.Check.input Source code
GSReg.DIRAC.Pathways Source code
GSReg.DIRAC.mu Source code
GSReg.GeneSets.DIRAC Man page Source code
GSReg.GeneSets.EVA Man page Source code
GSReg.Prune Source code
GSReg.SEVA Man page Source code
GSReg.Variance Source code
GSReg.kendall.tau.distance Man page Source code
GSReg.kendall.tau.distance.Restricted.Sparse.internal Source code
GSReg.kendall.tau.distance.Restricted.internal Source code
GSReg.kendall.tau.distance.internal Source code
GSReg.kendall.tau.distance.restricted Man page Source code
GSReg.kendall.tau.distance.template Source code
GSReg.kendall.tau.distance.template.internal Source code
GSReg.kendall.tau.template Man page
GSReg.overlapJunction Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/exportedFuncs.R
R/internalFuncs.R
build
build/vignette.rds
data
data/juncExprsSimulated.rda
inst
inst/doc
inst/doc/GSReg.R
inst/doc/GSReg.Rnw
inst/doc/GSReg.pdf
man
man/GSReg-package.Rd
man/GSReg_GeneSets_DIRAC.Rd
man/GSReg_GeneSets_VReg..Rd
man/GSReg_Kendall.Rd
man/GSReg_OverlapJunction.Rd
man/GSReg_SEVA.Rd
src
src/init.c
src/kendallTauDistance.cc
src/kendallTauDistanceFromTemp.cc
src/kendallTauDistanceRestricted.cc
src/nij.cc
src/vect2compC.cc
vignettes
vignettes/DIRAC.pdf
vignettes/DIRACAn.rda
vignettes/DIRAC_Parkinson.pdf
vignettes/DIRAC_comparison_squamous_GDS2520.pdf
vignettes/DIRACvsGSReg.pdf
vignettes/GSReg.Rnw
vignettes/GSReg.bib
vignettes/Rplots.pdf
vignettes/TheoreticalvsPermpvalue.pdf
vignettes/plots-011-1000perm.pdf
vignettes/plots-011-1000perm_Parkinsons.pdf
vignettes/plots-011.pdf
vignettes/plots-015-1000perm.pdf
vignettes/plots-016.pdf
GSReg documentation built on May 20, 2017, 11:01 p.m.