MotifDb
An Annotated Collection of Protein-DNA Binding Sequence Motifs
Bioconductor version: 3.23 · Package version: 1.54.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MotifDb")Details
| Maintainer | Paul Shannon <pshannon@systemsbiology.org> |
| Author | Paul Shannon, Matt Richards |
| License | Artistic-2.0 | file LICENSE |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | MotifAnnotation, Software |
| Package Short Url | https://bioconductor.org/packages/MotifDb/ |
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.
Documentation
Download
Follow the 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 (arm64) | MotifDb_1.54.0.tgz |
| macOS binary (x86_64) | MotifDb_1.54.0.tgz |
Dependencies
Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings
Imports: rtracklayer, splitstackshape
Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown
Reverse dependencies
Depends On Me (2): generegulation, motifbreakR
Suggests Me (15): ATACseqQC, DiffLogo, enhancerHomologSearch, igvR, memes, MMDiff2, motifcounter, motifStack, motifTestR, profileScoreDist, PWMEnrich, rTRM, TFutils, universalmotif, vtpnet