To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("MotIV")
In most cases, you don't need to download the package archive at all.
MotIV
Motif Identification and Validation
Bioconductor version: 3.0
This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.
Author: Eloi Mercier, Raphael Gottardo
Maintainer: Eloi Mercier <emercier at bcgsc.ca>, Raphael Gottardo <rgottard at fhcrc.org>
Citation (from within R,
enter citation("MotIV")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("MotIV")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MotIV")
| R Script | The MotIV users guide | |
| Reference Manual |
Details
| biocViews | ChIPSeq, ChIPchip, GenomicSequence, Microarray, MotifAnnotation, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) |
| License | GPL-2 |
| Depends | R (>= 2.10), BiocGenerics(>= 0.1.0) |
| Imports | graphics, grid, methods, IRanges(>= 1.13.5), Biostrings(>= 1.24.0), lattice, rGADEM, stats, utils |
| LinkingTo | |
| Suggests | rtracklayer |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | motifStack |
| Imports Me | |
| Suggests Me | MotifDb |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | MotIV_1.22.0.tar.gz |
| Windows Binary | MotIV_1.22.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | MotIV_1.22.0.tgz |
| Mac OS X 10.9 (Mavericks) | MotIV_1.22.0.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
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2015, Bioconductor
