RcisTarget

DOI: 10.18129/B9.bioc.RcisTarget  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see RcisTarget.

RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("RcisTarget")

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("RcisTarget")

 

HTML	R Script	RcisTarget - on regions
HTML	R Script	RcisTarget - with background
HTML	R Script	RcisTarget: Transcription factor binding motif enrichment
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneRegulation, GeneSetEnrichment, GeneTarget, MotifAnnotation, Software, Transcription, Transcriptomics
Version	1.20.0
In Bioconductor since	BioC 3.7 (R-3.5) (5.5 years)
License	GPL-3
Depends	R (>= 3.5.0)
Imports	AUCell(>= 1.1.6), BiocGenerics, data.table, graphics, GenomeInfoDb, GenomicRanges, arrow (>= 2.0.0), dplyr, tibble, GSEABase, methods, R.utils, stats, SummarizedExperiment, S4Vectors, utils
LinkingTo
Suggests	Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, gplots, rtracklayer, 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_1.20.0.tar.gz
Windows Binary	RcisTarget_1.20.0.zip
macOS Binary (x86_64)	RcisTarget_1.20.0.tgz
macOS Binary (arm64)	RcisTarget_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RcisTarget
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RcisTarget
Bioc Package Browser	https://code.bioconductor.org/browse/RcisTarget/
Package Short Url	https://bioconductor.org/packages/RcisTarget/
Package Downloads Report	Download Stats