HTSanalyzeR

DOI: 10.18129/B9.bioc.HTSanalyzeR    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.10 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: 3.10

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	CellBasedAssays, ImmunoOncology, MultipleComparison, Software
Version	2.38.0
In Bioconductor since	BioC 2.7 (R-2.12) (9.5 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
Links To Me
Build Report

Package Archives

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

Source Package	HTSanalyzeR_2.38.0.tar.gz
Windows Binary	HTSanalyzeR_2.38.0.zip
Mac OS X 10.11 (El Capitan)	HTSanalyzeR_2.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HTSanalyzeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HTSanalyzeR
Package Short Url	https://bioconductor.org/packages/HTSanalyzeR/
Package Downloads Report	Download Stats