To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cosmo")
In most cases, you don't need to download the package archive at all.
cosmo
|
This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see cosmo.
Supervised detection of conserved motifs in DNA sequences
Bioconductor version: 2.8
cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may include bounds on the information content across certain regions of the unknown motif, for example, and can often be formulated on the basis of prior knowledge about the structure of the transcription factor in question. The unknown motif width, the distribution of motif occurrences (OOPS, ZOOPS, or TCM), as well as the appropriate constraint set can be selected data-adaptively.
Author: Oliver Bembom, Fabian Gallusser, and Sandrine Dudoit
Maintainer: Oliver Bembom <oliver.bembom at gmail.com>
Citation (from within R,
enter citation("cosmo")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cosmo")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cosmo")
| cosmo.pdf | ||
| Reference Manual |
Details
| biocViews | SequenceMatching, Software |
| Version | 1.18.0 |
| In Bioconductor since | BioC 2.0 (R-2.5) (9 years) |
| License | file LICENSE |
| Depends | R (>= 2.4.0), methods, utils, seqLogo |
| Imports | |
| LinkingTo | |
| Suggests | cosmoGUI |
| SystemRequirements | |
| Enhances | |
| URL | http://cosmoweb.berkeley.edu/intro.html http://www.bepress.com/sagmb/vol6/iss1/art8 |
| Depends On Me | cosmoGUI |
| Imports Me | |
| Suggests Me | mosaics |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | cosmo_1.18.0.tar.gz |
| Windows Binary | cosmo_1.18.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/cosmo/tree/release-2.8 |
| Package Short Url | http://bioconductor.org/packages/cosmo/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
