GSCA: GSCA: Gene Set Context Analysis
Version 2.6.0

GSCA takes as input several lists of activated and repressed genes. GSCA then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. GSCA provides both traditional R functions and interactive, user-friendly user interface.

Browse man pages Browse package API and functions Browse package files

AuthorZhicheng Ji, Hongkai Ji
Bioconductor views GUI GeneExpression Visualization
Date of publicationNone
MaintainerZhicheng Ji <zji4@jhu.edu>
LicenseGPL(>=2)
Version2.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GSCA")

Man pages

annotatePeaks: Annotate ChIPx peaks with genes by Entrez GeneIDs
ConstructTG: Construct target genes for a TF using TF-bound genes and...
geneIDdata: Homologene data
GSCA: GSCA
GSCAeda: GSCA follow-up exploratory data analysis
GSCA-package: GSCA: Gene Set Context Analysis
GSCAplot: Visualize GSCA output
GSCAui: Launch GSCA interactive User Interface
Oct4ESC_TG: Oct4 activated (+) and repressed (-) target genes in...
STAT1_TG: STAT1 activated (+) target genes defined from experimental...
tabSearch: Searches through GPL96, GPL1261, GPL570 or GPL571 compendium...

Functions

ConstructTG Man page Source code
GSCA Man page Source code
GSCA-package Man page Man page
GSCAeda Man page Source code
GSCAplot Man page Source code
GSCAui Man page Source code
Oct4ESC_TG Man page
STAT1_TG Man page
annotatePeaks Man page Source code
geneIDdata Man page
tabSearch Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/ConstructTG.R
R/GSCA.R
R/GSCAeda.R
R/GSCAplot.R
R/GSCAui.R
R/annotatePeaks.R
R/tabSearch.R
README.md
build
build/vignette.rds
data
data/Oct4ESC_TG.rda
data/STAT1_TG.rda
data/geneIDdata.rda
inst
inst/CITATION
inst/doc
inst/doc/GSCA.R
inst/doc/GSCA.Rnw
inst/doc/GSCA.pdf
inst/extdata
inst/extdata/GSM288346_ES_Oct4.txt
inst/extdata/Pou5f1_E14TG2a_GSE4189_Limma.txt
inst/extdata/allreffile.rda
inst/shiny
inst/shiny/server.R
inst/shiny/ui.R
inst/shiny/www
inst/shiny/www/GSCAmanual.pdf
inst/shiny/www/ajaxloaderq.gif
inst/shiny/www/busy.js
inst/shiny/www/style.css
man
man/ConstructTG.Rd
man/GSCA-package.Rd
man/GSCA.Rd
man/GSCAeda.Rd
man/GSCAplot.Rd
man/GSCAui.Rd
man/Oct4ESC_TG.Rd
man/STAT1_TG.Rd
man/annotatePeaks.Rd
man/geneIDdata.Rd
man/tabSearch.Rd
vignettes
vignettes/GSCA.Rnw
GSCA documentation built on May 20, 2017, 10:47 p.m.