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
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Package details |
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| Author | Sara 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 |
| Maintainer | Gert Hulselmans <Gert.Hulselmans@kuleuven.be> |
| License | GPL-3 |
| Version | 1.23.1 |
| URL | http://scenic.aertslab.org |
| Package repository | View on GitHub |
| Installation |
Install the latest version of this package by entering the following in R:
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