RcisTarget

DOI:10.18129/B9.bioc.RcisTarget

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, seeRcisTarget.

RcisTarget: Identify transcription factor binding motifs enriched on a gene list

Bioconductor version: 3.8

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

Installation

To install this package, start R (version "3.5") and enter:

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

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

Documentation

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("RcisTarget")

HTML	R Script	RcisTarget: Transcription factor binding motif enrichment
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneRegulation,GeneSetEnrichment,GeneTarget,MotifAnnotation,Software,Transcription,Transcriptomics
Version	1.2.1
In Bioconductor since	BioC 3.7 (R-3.5) (1 year)
License	GPL-3
Depends	R (>= 3.4)
Imports	AUCell(>= 1.1.6),BiocGenerics,data.table,feather, graphics,GSEABase, methods,R.utils, stats,SummarizedExperiment, utils
LinkingTo
Suggests	Biobase,BiocStyle,BiocParallel,doParallel,DT,foreach,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
Suggests Me	universalmotif
Links To Me
Build Report

Package Archives

Followbob 体育网址 instructions to use this package in your R session.

Source Package	RcisTarget_1.2.1.tar.gz
Windows Binary	RcisTarget_1.2.1.zip(32- & 64-bit)
Mac OS X 10.11 (El Capitan)	RcisTarget_1.2.1.tgz
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	//www.anjoumacpherson.com/packages/RcisTarget/
Package Downloads Report	Download Stats