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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("HTSanalyzeR")
In most cases, you don't need to download the package archive at all.
HTSanalyzeR
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Gene set over-representation, enrichment and network analyses for high-throughput screens
Bioconductor version: Release (3.5)
This package provides classes and methods for gene set over-representation, enrichment and network analyses on high-throughput screens. The over-representation analysis is performed based on hypergeometric tests. The enrichment analysis is based on the GSEA algorithm (Subramanian et al. PNAS 2005). The network analysis identifies enriched subnetworks based on algorithms from the BioNet package (Beisser et al., Bioinformatics 2010). A pipeline is also specifically designed for cellHTS2 object to perform integrative network analyses of high-throughput RNA interference screens. The users can build their own analysis pipeline for their own data set based on this package.
Author: Xin Wang <xinwang2hms at gmail.com>, Camille Terfve <cdat2 at cam.ac.uk>, John C. Rose <jcr53 at cam.ac.uk>, Florian Markowetz <Florian.Markowetz at cruk.cam.ac.uk>
Maintainer: Xin Wang <xinwang2hms at gmail.com>
Citation (from within R,
enter citation("HTSanalyzeR")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("HTSanalyzeR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HTSanalyzeR")
| R Script | Main vignette:Gene set enrichment and network analysis of high-throughput RNAi screen data using HTSanalyzeR | |
| Reference Manual |
Details
| biocViews | CellBasedAssays, MultipleComparison, Software |
| Version | 2.28.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) (7 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.15), igraph, methods |
| Imports | graph, igraph, GSEABase, BioNet, cellHTS2, AnnotationDbi, biomaRt, RankProd |
| LinkingTo | |
| Suggests | KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | Mulder2012, phenoTest |
| Suggests Me | RTN |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HTSanalyzeR_2.28.0.tar.gz |
| Windows Binary | HTSanalyzeR_2.28.0.zip |
| Mac OS X 10.11 (El Capitan) | HTSanalyzeR_2.28.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HTSanalyzeR |
| Package Short Url | http://bioconductor.org/packages/HTSanalyzeR/ |
| Package Downloads Report | Download Stats |
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