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Bios2cor
View on CRAN: Click
here
Download and install Bios2cor package within the R console
Install from CRAN:
install.packages("Bios2cor")
Install from Github:
library("remotes")
install_github("cran/Bios2cor")
Install by package version:
library("remotes")
install_version("Bios2cor", "2.2.1")
Attach the package and use:
library("Bios2cor")
Maintained by
Marie Chabbert
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-08-24
Latest Update: 2022-07-08
Description:
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) and (2) Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M (2018) . An example of side chain correlated motion analysis is provided in: Taddese B, Garnier A, Abdi H, Henrion D, Chabbert M (2020) . This work was supported by the French National Research Agency (Grant number: ANR-11-BSV2-026) and by GENCI (Grant number: 100567).
How to cite:
Marie Chabbert (2017). Bios2cor: From Biological Sequences and Simulations to Correlation
Analysis. R package version 2.2.1, https://cran.r-project.org/web/packages/Bios2cor
Previous versions and publish date:
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Other R packages that Bios2cor depends,
imports, suggests or enhances
Functions, R codes and Examples using
the Bios2cor R package
Some associated functions: angle2rotamer . angles.plot . bios2cor-package . centered_pca . delta_filter . dynamic_circular . dynamic_entropy . dynamic_mi . dynamic_mip . dynamic_omes . dynamic_structure . elsc . entropy . import.fasta . import.msf . mcbasc . mi . mip . network.plot . omes . pca_2d . pca_screeplot . random.msa . scores.boxplot . scores_entropy.plot . top_pairs_analysis . write.entropy . write.pca . write.pca.pdb . write.scores . xyz2torsion .
Some associated R codes: angle2rotamer.R . angles.plot.R . centered_pca.R . delta_filter.R . dynamic_circular.R . dynamic_entropy.R . dynamic_mi.R . dynamic_mip.R . dynamic_omes.R . dynamic_structure.R . elsc.R . entropy.R . import.fasta.R . import.msf.R . mcbasc.R . mi.R . mip.R . network.plot.R . omes.R . pca_2d.R . pca_screeplot.R . random.msa.R . scores.boxplot.R . scores_entropy.plot.R . top_pairs_analysis.R . write.entropy.R . write.pca.R . write.pca.pdb.R . write.scores.R . xyz2torsion.R . Full Bios2cor package functions and examples
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