RcisTarget

DOI: 10.18129/B9.bioc.RcisTarget    

RcisTarget: Identify transcription factor binding motifs enriched on a gene list

Bioconductor version: Release (3.7)

RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).

Author: Sara Aibar, Gert Hulselmans, Stein Aerts. Laboratory of Computational Biology. VIB-KU Leuven Center for Brain & Disease Research. Leuven, Belgium

Maintainer: Sara Aibar <sara.aibar at kuleuven.vib.be>

Citation (from within R, enter citation("RcisTarget")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RcisTarget")

Documentation

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

browseVignettes("RcisTarget")

 

HTML R Script RcisTarget: Transcription factor binding motif enrichment
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneRegulation, GeneSetEnrichment, GeneTarget, MotifAnnotation, Software, Transcription, Transcriptomics
Version 1.0.2
License GPL-3
Depends R (>= 3.4)
Imports AUCell(>= 1.1.6), BiocGenerics, data.table, feather, graphics, GSEABase, methods, R.utils, stats, SummarizedExperiment, utils
LinkingTo
Suggests Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork
SystemRequirements
Enhances doMC, doRNG, zoo
URL http://scenic.aertslab.org
BugReports https://github.com/aertslab/RcisTarget/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package RcisTarget_1.0.2.tar.gz
Windows Binary RcisTarget_1.0.2.zip
Mac OS X 10.11 (El Capitan) RcisTarget_1.0.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/RcisTarget
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RcisTarget
Package Short Url http://bioconductor.org/packages/RcisTarget/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: