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

Bioconductor version: Release (3.18)

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")):


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Reference Manual PDF


biocViews GeneRegulation, GeneSetEnrichment, GeneTarget, MotifAnnotation, Software, Transcription, Transcriptomics
Version 1.22.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
System Requirements
URL http://scenic.aertslab.org
Bug Reports https://github.com/aertslab/RcisTarget/issues
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Suggests Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, gplots, rtracklayer, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork
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Enhances doMC, doRNG, zoo
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Source Package
Windows Binary RcisTarget_1.22.0.zip
macOS Binary (x86_64) RcisTarget_1.22.0.tgz
macOS Binary (arm64) RcisTarget_1.22.0.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/
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