CRAN/E | COUSCOus

COUSCOus

A Residue-Residue Contact Detecting Method

Installation

About

Contact prediction using shrinked covariance (COUSCOus). COUSCOus is a residue-residue contact detecting method approaching the contact inference using the glassofast implementation of Matyas and Sustik (2012, The University of Texas at Austin UTCS Technical Report 2012:1-3. TR-12-29.) that solves the L_1 regularised Gaussian maximum likelihood estimation of the inverse of a covariance matrix. Prior to the inverse covariance matrix estimation we utilise a covariance matrix shrinkage approach, the empirical Bayes covariance estimator, which has been shown by Haff (1980) doi:10.1214/aos/1176345010 to be the best estimator in a Bayesian framework, especially dominating estimators of the form aS, such as the smoothed covariance estimator applied in a related contact inference technique PSICOV.

Key Metrics

Version 1.0.0
R ≥ 3.2.2
Published 2016-02-28 2971 days ago
Needs compilation? yes
License GPL (≥ 3)
CRAN checks COUSCOus results

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Maintainer

Maintainer

Reda Rawi

rrawi@qf.org.qa

Authors

Reda Rawi

aut / cre

Matyas A. Sustik

aut

Ben Calderhead

aut

Material

Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Depends

R ≥ 3.2.2

Imports

bio3d ≥ 2.2-2
matrixcalc ≥ 1.0-3
utils ≥ 3.2.2