CorMut
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CorMut.
Detect the correlated mutations based on selection pressure
Bioconductor version: 3.9
CorMut provides functions for computing kaks for individual sites or specific amino acids and detecting correlated mutations among them. Three methods are provided for detecting correlated mutations ,including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; Second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network. The reference sequence should be the first sequence of the sequence file, and does not allow the presence of gap.
Author: Zhenpeng Li
Maintainer: Zhenpeng Li<zpli21 at gmail.com>
citation("CorMut")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CorMut")
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("CorMut")| CorMut | R Script | |
| Reference Manual |
Details
| biocViews | Sequencing, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (11.5 years) |
| License | GPL-2 |
| Depends | methods, seqinr, igraph |
| Imports | |
| System Requirements | |
| URL |
See More
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| Enhances | |
| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CorMut_1.26.0.tar.gz |
| Windows Binary | CorMut_1.26.0.zip |
| Mac OS X 10.11 (El Capitan) | CorMut_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CorMut |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CorMut |
| Bioc Package Browser | https://code.bioconductor.org/browse/CorMut/ |
| Package Short Url | https://bioconductor.org/packages/CorMut/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |