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

Bioconductor version: Release (3.19)

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: Gert Hulselmans <Gert.Hulselmans at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


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


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

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


biocViews GeneRegulation, GeneSetEnrichment, GeneTarget, MotifAnnotation, Software, Transcription, Transcriptomics
Version 1.24.0
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, zoo
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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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Source Package RcisTarget_1.24.0.tar.gz
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macOS Binary (arm64) RcisTarget_1.24.0.tgz
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