Package: GSCA 2.43.1

Zhicheng Ji

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.

Authors:Zhicheng Ji, Hongkai Ji

GSCA_2.43.1.tar.gz
GSCA_2.43.1.zip(r-4.7-any)GSCA_2.43.1.zip(r-4.6-any)GSCA_2.43.1.zip(r-4.5-any)
GSCA_2.43.1.tgz(r-4.6-any)GSCA_2.43.1.tgz(r-4.5-any)
GSCA_2.43.1.tar.gz(r-4.7-any)GSCA_2.43.1.tar.gz(r-4.6-any)
GSCA_2.43.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GSCA/json (API)

# Install 'GSCA' in R:

install.packages('GSCA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

geneIDdata - Homologene data
Oct4ESC_TG - Oct4 activated (+) and repressed (-) target genes in embryonic stem cells
STAT1_TG - STAT1 activated (+) target genes defined from experimental ChIP-seq data and literature survey.

On BioConductor:GSCA-2.43.1(bioc 3.24)GSCA-2.42.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpression visualization gui

5.22 score 11 scripts 504 downloads 40 mentions 7 exports 58 dependencies

Last updated from:94bd64f110. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	224
linux-devel	NOTE	305
source / vignettes	OK	300
linux-release	NOTE	274
macos-release	NOTE	196
macos-oldrel	NOTE	199
windows-devel	NOTE	223
windows-release	NOTE	210
windows-oldrel	NOTE	205
wasm-release	OK	158

Exports:annotatePeaks ConstructTG GSCA GSCAeda GSCAplot GSCAui tabSearch

Dependencies:base64enc biocmake bitops bslib cachem caTools cli commonmark cpp11 digest dir.expiry farver fastmap filelock fontawesome fs ggplot2 glue gplots gtable gtools htmltools httpuv isoband jquerylib jsonlite KernSmooth labeling later lattice lifecycle magrittr memoise mime otel plyr promises R6 rappdirs RColorBrewer Rcpp reshape2 rhdf5 rhdf5filters Rhdf5lib rlang S7 sass scales shiny sourcetools sp stringi stringr vctrs viridisLite withr xtable

GSCA

Rendered fromGSCA.Rnwusingutils::Sweave

Last update: 2015-12-08
Started: 2014-02-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
GSCA: Gene Set Context Analysis	GSCA-package
Annotate ChIPx peaks with genes by Entrez GeneIDs	annotatePeaks
Construct target genes for a TF using TF-bound genes and differentially expressed genes from ChIP-chip or ChIP-seq and TF perturbation gene expression data.	ConstructTG
Homologene data	geneIDdata
GSCA	GSCA
GSCA follow-up exploratory data analysis	GSCAeda
Visualize GSCA output	GSCAplot
Launch GSCA interactive User Interface	GSCAui
Oct4 activated (+) and repressed (-) target genes in embryonic stem cells	Oct4ESC_TG
STAT1 activated (+) target genes defined from experimental ChIP-seq data and literature survey.	STAT1_TG
Searches through GPL96, GPL1261, GPL570 or GPL571 compendium data for biological contexts of interest.	tabSearch