HTSanalyzeR

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see HTSanalyzeR.

Gene set over-representation, enrichment and network analyses for high-throughput screens


Bioconductor version: 3.9

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 (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HTSanalyzeR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("HTSanalyzeR")
Main vignette:Gene set enrichment and network analysis of high-throughput RNAi screen data using HTSanalyzeR PDF R Script
Reference Manual PDF

Details

biocViews CellBasedAssays, ImmunoOncology, MultipleComparison, Software
Version 2.36.0
In Bioconductor since BioC 2.7 (R-2.12) (13.5 years)
License Artistic-2.0
Depends R (>= 2.15), igraph, methods
Imports graph, igraph, GSEABase, BioNet, cellHTS2, AnnotationDbi, biomaRt, RankProd
System Requirements
URL
See More
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
Linking To
Enhances
Depends On Me
Imports Me Mulder2012, phenoTest
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HTSanalyzeR_2.36.0.tar.gz
Windows Binary HTSanalyzeR_2.36.0.zip
Mac OS X 10.11 (El Capitan) HTSanalyzeR_2.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/HTSanalyzeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HTSanalyzeR
Bioc Package Browser https://code.bioconductor.org/browse/HTSanalyzeR/
Package Short Url https://bioconductor.org/packages/HTSanalyzeR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive