R Observatory: Metrics for Bios2cor version 2.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Bios2cor

2.2.2Package record

From Biological Sequences and Simulations to Correlation Analysis

0packages depend

7.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Marie ChabbertCRAN page ↗

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).

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

install.packages("Bios2cor", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-bios2cor

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-Bios2cor

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.7 min · r-release-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2.2

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 31includes a package overview page
Examples that run: 100%31 run in a plain check
Exported functions with examples: 100%
Documented parameters: 92%
Return-value docs: 100%
Help pages citing references: 52%

How these are measured

Downloads

7.3K

CRAN downloads in the past year

Rank #6,309 · ~20/day · ~612/mo

Releases R versions

Daily download trend is not available in this view yet.

50430 days

1.3K90 days

7.3K1 year

Compare downloads with other packages →

Also on1.4K r2u

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing Bios2cor adds 17 packages (12 with compiled code, 27 MB of source tarballs). Heaviest: BH 14 MB, igraph 4.8 MB, Rcpp 1.8 MB.

Depends (5)

R >= 3.5bio3d circular bigmemoryparallel

Imports (1)

igraph

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (7)

Marie Chabbert

Author, Maintainer since 1.1 (2017)

Author

Author

Author

Contributor

Contributor

Contributor

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
unarchivedReturned to CRAN
2024-11-14
2.2.2Latest
record
2024-11-14 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2024-04-20
issues were not corrected despite reminders
R
R 4.3.0 released · 2023-04-21
2.2.1
record
2022-07-08 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
2.2
record
2020-10-02 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.1
record
2020-01-30 · diff ↗
2.0
record
2019-10-31 · diff ↗ ·
removed 23 exports
ang_evo_graph, angle_conversion, corr_contact, create_boxplot, create_corrfile, create_entropyfile, create_network, create_pcafile, create_screeplot, cyto_entropy, cyto_zscore, delta_weighting, dynamic_struct, entropy_graph, gauss_weighting, rotamer_circular, rotamer_entropy, rotamer_mip, rotamer_omes, shuffle_all, shuffle_positions, sigmoid_weighting, write_pdb

added 19 exports
angles.plot, angle2rotamer, top_pairs_analysis, scores.boxplot, write.scores, write.entropy, network.plot, write.pca, pca_screeplot, delta_filter, dynamic_structure, scores_entropy.plot, mi, dynamic_circular, dynamic_mi, dynamic_mip, dynamic_omes, dynamic_entropy, write.pca.pdb
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23

Show 5 earlier eventsHide 5 earlier events

unarchivedReturned to CRAN
2017-09-07
1.2
record
2017-09-07 · diff ↗
archivedRemoved from CRAN
2017-08-26
policy violation
1.1
record
2017-08-24
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-08-24
Total releases: 7 / 9 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5
Download size: 863 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Bios2cor")

Format

Chabbert, M., Becu, J., Bellenger, L., Deniaud, M., Garnier, A., Pele, J., & Taddese, B. (2024). Bios2cor: From Biological Sequences and Simulations to Correlation Analysis (Version 2.2.2) [Computer software]. https://doi.org/10.32614/CRAN.package.Bios2cor

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for Bios2cor version 2.2.2 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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