MotifDb

DOI: 10.18129/B9.bioc.MotifDb  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see MotifDb.

An Annotated Collection of Protein-DNA Binding Sequence Motifs

Bioconductor version: 3.16

More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.

Author: Paul Shannon, Matt Richards

Maintainer: Paul Shannon <pshannon at systemsbiology.org>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("MotifDb")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MotifDb")

 

HTML	R Script	A collection of PWMs
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	MotifAnnotation, Software
Version	1.40.0
In Bioconductor since	BioC 2.11 (R-2.15) (10.5 years)
License	Artistic-2.0 | file LICENSE
Depends	R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
Imports	rtracklayer, splitstackshape
LinkingTo
Suggests	RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown
SystemRequirements
Enhances
URL
Depends On Me	generegulation, motifbreakR, trena
Imports Me	rTRMui
Suggests Me	ATACseqQC, DiffLogo, enhancerHomologSearch, igvR, memes, MMDiff2, motifcounter, motifStack, profileScoreDist, PWMEnrich, rTRM, TFutils, universalmotif, vtpnet
Links To Me
Build Report

Package Archives

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

Source Package	MotifDb_1.40.0.tar.gz
Windows Binary	MotifDb_1.40.0.zip (64-bit only)
macOS Binary (x86_64)	MotifDb_1.40.0.tgz
macOS Binary (arm64)	MotifDb_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MotifDb
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MotifDb
Bioc Package Browser	https://code.bioconductor.org/browse/MotifDb/
Package Short Url	https://bioconductor.org/packages/MotifDb/
Package Downloads Report	Download Stats