Package: Bios2cor 2.2.2
Marie Chabbert
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).
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Bios2cor_2.2.2.tar.gz
Bios2cor_2.2.2.tar.gz(r-4.5-noble)Bios2cor_2.2.2.tar.gz(r-4.4-noble)
Bios2cor_2.2.2.tgz(r-4.4-emscripten)Bios2cor_2.2.2.tgz(r-4.3-emscripten)
Bios2cor.pdf |Bios2cor.html✨
Bios2cor/json (API)
# Install 'Bios2cor' in R: |
install.packages('Bios2cor', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 1 months agofrom:9b8bb86fda. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 15 2024 |
R-4.5-linux | OK | Dec 15 2024 |
Exports:angle2rotamerangles.plotcentered_pcadelta_filterdynamic_circulardynamic_entropydynamic_midynamic_mipdynamic_omesdynamic_structureelscentropyimport.fastaimport.msfmcbascmimipnetwork.plotomespca_2dpca_screeplotrandom.msascores_entropy.plotscores.boxplottop_pairs_analysiswrite.entropywrite.pcawrite.pca.pdbwrite.scoresxyz2torsion
Dependencies:BHbigmemorybigmemory.sribio3dbootcircularclicpp11glueigraphlatticelifecyclemagrittrMatrixmvtnormpkgconfigRcpprlanguuidvctrs