MatrixRider
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MatrixRider.
Obtain total affinity and occupancies for binding site matrices on a given sequence
Bioconductor version: 3.9
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("MatrixRider")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MatrixRider")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MatrixRider")| Total affinity and occupancies | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneRegulation, Genetics, MotifAnnotation, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | GPL-3 |
| Depends | R (>= 3.1.2) |
| Imports | methods, TFBSTools, IRanges, XVector, Biostrings |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocGenerics, BiocStyle, JASPAR2014 |
| Linking To | IRanges, XVector, Biostrings, S4Vectors |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MatrixRider_1.16.0.tar.gz |
| Windows Binary | MatrixRider_1.16.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | MatrixRider_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MatrixRider |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MatrixRider |
| Bioc Package Browser | https://code.bioconductor.org/browse/MatrixRider/ |
| Package Short Url | https://bioconductor.org/packages/MatrixRider/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |