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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("PWMEnrich")
In most cases, you don't need to download the package archive at all.
PWMEnrich
PWM enrichment analysis
Bioconductor version: 2.14
A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.
Author: Robert Stojnic, Diego Diez
Maintainer: Robert Stojnic <robert.stojnic at gmail.com>
Citation (from within R,
enter citation("PWMEnrich")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("PWMEnrich")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PWMEnrich")
| R Script | Overview of the 'PWMEnrich' package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GenomicSequence, SequenceMatching, Software |
| Version | 3.6.1 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | LGPL (>= 2) |
| Depends | methods, grid, BiocGenerics, Biostrings |
| Imports | seqLogo, gdata, evd |
| Suggests | MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel |
| System Requirements | |
| URL | |
| Depends On Me | PWMEnrich.Dmelanogaster.background, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background |
| Imports Me | |
| Suggests Me | rTRM |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | PWMEnrich_3.6.1.tar.gz |
| Windows Binary | PWMEnrich_3.6.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | PWMEnrich_3.6.1.tgz |
| Mac OS X 10.9 (Mavericks) | PWMEnrich_3.6.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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