Package: COUSCOus
Type: Package
Title: A Residue-Residue Contact Detecting Method
Version: 1.0.0
Date: 2016-02-17
Author: Reda Rawi [aut,cre], Matyas A. Sustik [aut], Ben Calderhead [aut]
Maintainer: Reda Rawi <rrawi@qf.org.qa>
Description: 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.
Repository: CRAN
License: GPL (>= 3)
Imports: bio3d (>= 2.2-2), matrixcalc (>= 1.0-3), utils (>= 3.2.2)
Depends: R (>= 3.2.2)
NeedsCompilation: yes
Packaged: 2016-02-28 13:00:30 UTC; reda
Date/Publication: 2016-02-28 16:26:52
Built: R 4.0.2; x86_64-apple-darwin17.0; 2020-07-15 23:50:19 UTC; unix
Archs: COUSCOus.so.dSYM
