MotifDb
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see MotifDb.
An Annotated Collection of Protein-DNA Binding Sequence Motifs
Bioconductor version: 3.11
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 "4.0") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | MotifAnnotation, Software |
| Version | 1.30.0 |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | generegulation, motifbreakR, trena |
| Imports Me | igvR, rTRMui |
| Suggests Me | ATACseqQC, DiffLogo, 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_1.30.0.tar.gz |
| Windows Binary | MotifDb_1.30.0.zip |
| macOS 10.13 (High Sierra) | MotifDb_1.30.0.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 |
| Old Source Packages for BioC 3.11 | Source Archive |