Welcome to the new bioconductor.org!

RcisTarget

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")):

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

Reference Manual PDF

Details

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
See More
Suggests Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, gplots, rtracklayer, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork
Linking To
Enhances doMC, doRNG, zoo
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

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/
Package Downloads Report Download Stats