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 regionsBioconductor version: Development (3.22)
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 kuleuven.be>
Citation (from within R, entercitation("RcisTarget")
): Installation
To install this package, start R (version "4.5") and enter:
if (!require("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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RcisTarget")
Details biocViews GeneRegulation, GeneSetEnrichment, GeneTarget, MotifAnnotation, Software, Transcription, Transcriptomics Version 1.29.0 In Bioconductor since BioC 3.7 (R-3.5) (7 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 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 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.
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