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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("motifStack")
In most cases, you don't need to download the package archive at all.
motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Bioconductor version: 2.14
The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.
Author: Jianhong Ou, Michael Brodsky, Scot Wolfe and Lihua Julie Zhu
Maintainer: Jianhong Ou <jianhong.ou at umassmed.edu>
Citation (from within R,
enter citation("motifStack")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("motifStack")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("motifStack")
| R Script | motifStack Vignette | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GenomicsSequence, SequenceMatching, Software, Visualization |
| Version | 1.8.1 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | GPL (>= 2) |
| Depends | R (>= 2.15.1), methods, grImport, grid, MotIV, ade4 |
| Imports | XML |
| Suggests | RUnit, BiocGenerics, MotifDb, RColorBrewer, BiocStyle |
| System Requirements | |
| URL | |
| Depends On Me | dagLogo |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | motifStack_1.8.1.tar.gz |
| Windows Binary | motifStack_1.8.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | motifStack_1.8.1.tgz |
| Mac OS X 10.9 (Mavericks) | motifStack_1.8.1.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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