RcisTarget

DOI: 10.18129/B9.bioc.RcisTarget    

This is the development version of RcisTarget; for the stable release version, see RcisTarget.

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

Bioconductor version: Development (3.15)

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 "4.2") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("RcisTarget")

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

Documentation

PDF   Reference Manual

Details

biocViews GeneRegulation, GeneSetEnrichment, GeneTarget, MotifAnnotation, Software, Transcription, Transcriptomics
Version 1.15.0
In Bioconductor since BioC 3.7 (R-3.5) (3.5 years)
License GPL-3
Depends R (>= 3.4)
Imports AUCell(>= 1.1.6), BiocGenerics, data.table, feather, graphics, GenomeInfoDb, GenomicRanges, arrow (>= 2.0.0), dplyr, tibble, GSEABase, methods, R.utils, stats, SummarizedExperiment, utils
LinkingTo
Suggests Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, gplots, rtracklayer, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork
SystemRequirements
Enhances doMC, doRNG, zoo
URL http://scenic.aertslab.org
BugReports https://github.com/aertslab/RcisTarget/issues
Depends On Me
Imports Me
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Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/RcisTarget
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RcisTarget
Package Short Url https://bioconductor.org/packages/RcisTarget/
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