CorMut

Detect the correlated mutations based on selection pressure

Bioconductor version: Development (3.0)

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.

Author: Zhenpeng Li, Yang Huang, Yabo Ouyang, Yiming Shao, Liying Ma

Maintainer: Zhenpeng Li<zpli21 at gmail.com>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("CorMut")

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

Documentation

PDF R Script CorMut
PDF   Reference Manual

Details

biocViews Sequencing, Software
Version 1.7.0
In Bioconductor since BioC 2.11 (R-2.15)
License GPL-2
Depends seqinr, igraph
Imports
Suggests
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source CorMut_1.7.0.tar.gz
Windows Binary CorMut_1.7.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) CorMut_1.7.0.tgz
Mac OS X 10.9 (Mavericks) CorMut_1.7.0.tgz
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