GSCA: GSCA: Gene Set Context Analysis

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.

Author
Zhicheng Ji, Hongkai Ji
Date of publication
None
Maintainer
Zhicheng Ji <zji4@jhu.edu>
License
GPL(>=2)
Version
2.4.0

View on Bioconductor

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...

Files in this package

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