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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 |
| Reference manual: | Bios2cor.pdf |
| Package source: | Bios2cor_2.2.2.tar.gz |
| Windows binaries: | r-devel: Bios2cor_2.2.2.zip, r-release: Bios2cor_2.2.2.zip, r-oldrel: Bios2cor_2.2.2.zip |
| macOS binaries: | r-release (arm64): Bios2cor_2.2.2.tgz, r-oldrel (arm64): Bios2cor_2.2.2.tgz, r-release (x86_64): Bios2cor_2.2.2.tgz, r-oldrel (x86_64): Bios2cor_2.2.2.tgz |
| Old sources: | Bios2cor archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.