To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GSCA")
In most cases, you don't need to download the package archive at all.
GSCA
GSCA: Gene Set Context Analysis
Bioconductor version: 3.0
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.
Author: Zhicheng Ji, Hongkai Ji
Maintainer: Zhicheng Ji <zji4 at jhu.edu>
Citation (from within R,
enter citation("GSCA")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GSCA")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GSCA")
| R Script | GSCA | |
| Reference Manual |
Details
| biocViews | GUI, GeneExpression, Software, Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | GPL(>=2) |
| Depends | shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5, rgl, shinyRGL |
| Imports | graphics |
| LinkingTo | |
| Suggests | Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GSCA_1.4.0.tar.gz |
| Windows Binary | GSCA_1.4.0.zip |
| Mac OS X 10.6 (Snow Leopard) | GSCA_1.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | GSCA_1.4.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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