CorMut

DOI: 10.18129/B9.bioc.CorMut    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of CorMut; for the stable release version, see CorMut.

Detect the correlated mutations based on selection pressure

Bioconductor version: Development (3.12)

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 (from within R, enter citation("CorMut")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CorMut")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews Sequencing, Software
Version 1.31.1
In Bioconductor since BioC 2.11 (R-2.15) (8 years)
License GPL-2
Depends methods, seqinr, igraph
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/CorMut
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CorMut
Package Short Url https://bioconductor.org/packages/CorMut/
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