# COUSCOus: A Residue-Residue Contact Detecting Method

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.

- Author
- Reda Rawi [aut,cre], Matyas A. Sustik [aut], Ben Calderhead [aut]
- Date of publication
- 2016-02-28 16:26:52
- Maintainer
- Reda Rawi <rrawi@qf.org.qa>
- License
- GPL (>= 3)
- Version
- 1.0.0

## Man pages

- COUSCOus
- Contact prediction using shrinked covariance.
- COUSCOus-internal
- Internal COUSCOus functions

## Files in this package

COUSCOus |

COUSCOus/inst |

COUSCOus/inst/examples |

COUSCOus/inst/examples/1oaiA0.fa |

COUSCOus/src |

COUSCOus/src/calculate_single_site_frequencies.c |

COUSCOus/src/aa2num.c |

COUSCOus/src/glassofast.f90 |

COUSCOus/src/form_covarience_matrix.c |

COUSCOus/src/calculate_sequence_weights.c |

COUSCOus/src/guess_rho_matrix.c |

COUSCOus/src/calculate_pair_site_frequencies.c |

COUSCOus/NAMESPACE |

COUSCOus/R |

COUSCOus/R/helper_preprocess.R |

COUSCOus/R/helper_precision.R |

COUSCOus/R/helper_shrinkage.R |

COUSCOus/R/COUSCOus.R |

COUSCOus/R/helper_prediction.R |

COUSCOus/MD5 |

COUSCOus/DESCRIPTION |

COUSCOus/man |

COUSCOus/man/COUSCOus-internal.Rd |

COUSCOus/man/COUSCOus.Rd |