Utilities for computation and analysis of correlation/co-variation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/co-variation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and to analyze the correlation/co-variation 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 co-variation analysis and utility tools are provided in: Pele J, Moreau M, Abdi H, Rodien P, Castel H, Chabbert M. (2014) <doi:10.1002/prot.24570>. This work was supported by the French National Research Agency (Grant number: ANR-11-BSV2-026).
| Version: | 1.2 |
| Depends: | R (≥ 3.1), bio3d, circular, bigmemory, parallel |
| Imports: | igraph |
| Published: | 2017-09-07 |
| Author: | Bruck Taddese [aut], Antoine Garnier [aut], Madeline Deniaud [aut], Julien Pele [ctb], Lea Bellenger [ctb], Jean-Michel Becu [ctb], Marie Chabbert [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 |
| Reference manual: | Bios2cor.pdf |
| Package source: | Bios2cor_1.2.tar.gz |
| Windows binaries: | r-devel: Bios2cor_1.2.zip, r-release: Bios2cor_1.2.zip, r-oldrel: Bios2cor_1.2.zip |
| OS X El Capitan binaries: | r-release: Bios2cor_1.2.tgz |
| OS X Mavericks binaries: | r-oldrel: Bios2cor_1.2.tgz |
| Old sources: | Bios2cor archive |
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