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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MatrixRider")
In most cases, you don't need to download the package archive at all.
MatrixRider
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Obtain total affinity and occupancies for binding site matrices on a given sequence
Bioconductor version: Release (3.5)
Calculates a single number for a whole sequence that reflects the propensity of a DNA binding protein to interact with it. The DNA binding protein has to be described with a PFM matrix, for example gotten from Jaspar.
Author: Elena Grassi
Maintainer: Elena Grassi <grassi.e at gmail.com>
Citation (from within R,
enter citation("MatrixRider")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MatrixRider")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MatrixRider")
| R Script | Total affinity and occupancies | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneRegulation, Genetics, MotifAnnotation, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (2.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.1.2) |
| Imports | methods, TFBSTools, IRanges, XVector, Biostrings |
| LinkingTo | IRanges, XVector, Biostrings, S4Vectors |
| Suggests | RUnit, BiocGenerics, BiocStyle, JASPAR2014 |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MatrixRider_1.8.0.tar.gz |
| Windows Binary | MatrixRider_1.8.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | MatrixRider_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MatrixRider |
| Package Short Url | http://bioconductor.org/packages/MatrixRider/ |
| Package Downloads Report | Download Stats |
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