bios2cor-package |
Correlation/covariation Analysis in Biological Sequences and Simulations |

angle2rotamer |
Converts dihedral angles to rotamers |

angles.plot |
plots the time evolution of the dihedral angles in top pairs |

Bios2cor |
Correlation/covariation Analysis in Biological Sequences and Simulations |

bios2cor |
Correlation/covariation Analysis in Biological Sequences and Simulations |

centered_pca |
Performs principal component analysis of a correlation/covariation matrix |

delta_filter |
Creation of an entropy/dynamic score delta filter for each element |

dynamic_circular |
Circular correlation |

dynamic_entropy |
Variability score |

dynamic_mi |
Mutual Information (MI) function applied to rotamers in molecular dynamics simulations |

dynamic_mip |
Mutual Information Product (MIP) function applied to rotamers in molecular dynamics simulations |

dynamic_omes |
OMES (Observed minus Expected Squared) function applied to rotamers in molecular dynamics simulations |

dynamic_structure |
Creates the data structure for the analysis of side chain dihedral angles |

elsc |
Explicit Likelihood of Subset Covariation (ELSC) function |

entropy |
Entropy score |

import.fasta |
Reads a file in FASTA format |

import.msf |
Reads a multiple sequence alignment file in MSF format |

mcbasc |
McBASC (McLachlan Based Substitution Correlation) function |

mi |
Mutual Information (MI) function |

mip |
Mutual Information product (MIP) function |

network.plot |
Creates network structure of top elements |

omes |
OMES (Observed minus Expected Squared) function |

pca_2d |
PCA projection on two dimensions |

pca_screeplot |
Creates PCA screeplot |

random.msa |
Random Alignment |

scores.boxplot |
Creates boxplots of correlation/covariation scores |

scores_entropy.plot |
Scores versus entropy graph |

top_pairs_analysis |
Calculates the number of contacts for each element of the top pairs |

write.entropy |
Writes and displays entropy values |

write.pca |
Creates a file of coordinates in PCA space |

write.pca.pdb |
PDB and PML file creation for 3D representation of PCA analysis |

write.scores |
Creates a correlation/covariation ouput file |

xyz2torsion |
Convert Cartesian Coordinates to Torsion Angles |