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

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).

Getting started

Package details

AuthorSara Aibar, Gert Hulselmans, Stein Aerts. Laboratory of Computational Biology. VIB-KU Leuven Center for Brain & Disease Research. Leuven, Belgium
Bioconductor views GeneRegulation GeneSetEnrichment GeneTarget MotifAnnotation Transcription Transcriptomics
MaintainerSara Aibar <sara.aibar@kuleuven.vib.be>
LicenseGPL-3
Version1.11.10
URL http://scenic.aertslab.org
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("aertslab/RcisTarget")
aertslab/RcisTarget documentation built on April 21, 2021, 9:46 a.m.