Bios2cor: From Biological Sequences and Simulations to Correlation
Analysis
Utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and utilities to analyze the correlation/covariation matrix through a variety of tools including network representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation. Examples of sequence covariation analysis are provided in: (1) Pele J, Moreau M, Abdi H, Rodien P, Castel H, Chabbert M (2014) <doi:10.1002/prot.24570> and (2) Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M (2018) <doi:10.1371/journal.pcbi.1006209>. An example of side chain correlated motion analysis is provided in: Taddese B, Garnier A, Abdi H, Henrion D, Chabbert M (2020) <doi:10.1038/s41598-020-72766-1>. This work was supported by the French National Research Agency (Grant number: ANR-11-BSV2-026) and by GENCI (Grant number: 100567).
| Version: |
2.2.2 |
| Depends: |
R (≥ 3.5), bio3d, circular, bigmemory, parallel |
| Imports: |
igraph |
| Published: |
2024-11-14 |
| DOI: |
10.32614/CRAN.package.Bios2cor |
| Author: |
Bruck Taddese [aut],
Antoine Garnier [aut],
Madeline Deniaud [aut],
Julien Pele [ctb],
Lea Bellenger [ctb],
Jean-Michel Becu [ctb],
Marie Chabbert [aut, cre] |
| Maintainer: |
Marie Chabbert <marie.chabbert at univ-angers.fr> |
| License: |
GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: |
no |
| CRAN checks: |
Bios2cor results |
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