MotifDb

This is the released version of MotifDb; for the devel version, see MotifDb.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11

An Annotated Collection of Protein-DNA Binding Sequence Motifs

Bioconductor version: Release (3.23)

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>

Citation (from within R, enter citation("MotifDb")):

Paul Shannon, Matt Richards. MotifDb: An Annotated Collection of Protein-DNA Binding Sequence Motifs. doi:10.18129/B9.bioc.MotifDb, R package version 1.54.0, https://bioconductor.org/packages/MotifDb.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	MotifAnnotation, Software
Version	1.54.0
In Bioconductor since	BioC 2.11 (R-2.15) (14 years)
License	Artistic-2.0 \| file LICENSE
Depends	R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
Imports	rtracklayer, splitstackshape
System Requirements
URL

Suggests	RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown
Linking To
Enhances
Depends On Me	generegulation, motifbreakR
Imports Me	rTRMui, TENET
Suggests Me	ATACseqQC, DiffLogo, enhancerHomologSearch, igvR, memes, MMDiff2, motifcounter, motifStack, motifTestR, profileScoreDist, PWMEnrich, rTRM, TFutils, universalmotif, vtpnet
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	MotifDb_1.54.0.tar.gz
Windows Binary (x86_64)	MotifDb_1.54.0.zip
macOS Binary (big-sur-x86_64)	MotifDb_1.54.0.tgz
macOS Binary (sonoma-arm64)	MotifDb_1.54.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MotifDb
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MotifDb
Package Short Url	https://bioconductor.org/packages/MotifDb/
Package Downloads Report	Download Stats