MatrixRider
Obtain total affinity and occupancies for binding site matrices on a given sequence
Bioconductor version: Release (3.19)
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 (version "4.4") 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 | 1.36.0 |
In Bioconductor since | BioC 3.1 (R-3.2) (9.5 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_1.36.0.tar.gz |
Windows Binary | MatrixRider_1.36.0.zip (64-bit only) |
macOS Binary (x86_64) | MatrixRider_1.36.0.tgz |
macOS Binary (arm64) | |
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 |