Bios2cor

2.2.2

From Biological Sequences and Simulations to Correlation Analysis

0packages depend

8.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Marie ChabbertFirst published 2017-08-247 releasesCRAN 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.

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

Slowest check: 2.8 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 92%
Return-value docs: 100%
References docs: 52%

Downloads

8.2K

CRAN downloads in the past year

Rank #5,142 · ~22/day · ~680/mo

Releases R versions

Daily download trend is not available in this view yet.

41630 days

1.8K90 days

8.2K1 year

Compare downloads with other packages →

Also on1.4K r2u

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (7)

Maintainer (1)

Marie Chabbert

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Contributors (3)

Jean-Michel Becu

Contributor

Lea Bellenger

Contributor

Julien Pele

Contributor

Package Timeline

7 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
2.2.2Latest
2024-11-14 · current release · diff ↗
unarchivedReturned to CRAN
2024-11-14
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
2022-07-08 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
2.2
2020-10-02 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.1
2020-01-30 · diff ↗
2.0
2019-10-31 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23

Show 5 earlier events

1.2
2017-09-07 · diff ↗
unarchivedReturned to CRAN
2017-09-07
archivedRemoved from CRAN
2017-08-26
policy violation
1.1
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
Installed size: not tracked yet
With dependencies: not tracked yet

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