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MotifDb

An Annotated Collection of Protein-DNA Binding Sequence Motifs


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") 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

Details

biocViews MotifAnnotation, Software
Version 1.44.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License Artistic-2.0 | file LICENSE
Depends R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
Imports rtracklayer, splitstackshape
System Requirements
URL
See More
Suggests RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown
Linking To
Enhances
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 Build Report

Package Archives

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

Source Package MotifDb_1.44.0.tar.gz
Windows Binary MotifDb_1.44.0.zip
macOS Binary (x86_64) MotifDb_1.44.0.tgz
macOS Binary (arm64) MotifDb_1.44.0.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