R Observatory: Metrics for seq2R version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

seq2R

2.0.1

Simple Method to Detect Compositional Changes in Genomic Sequences

0packages depend

2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Nora M. VillanuevaFirst published 2012-08-234 releasesCRAN page ↗

This software is useful for loading '.fasta' or '.gbk' files, and for retrieving sequences from 'GenBank' dataset https://www.ncbi.nlm.nih.gov/genbank/. This package allows to detect differences or asymmetries based on nucleotide composition by using local linear kernel smoothers. Also, it is possible to draw inference about critical points (i. e. maximum or minimum points) related with the derivative curves. Additionally, bootstrap methods have been used for estimating confidence intervals and speed computational techniques (binning techniques) have been implemented in 'seq2R'.

Install

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

install.packages("seq2R", 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-seq2r

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-seq2R

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

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

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-seq2R

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.1 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

1

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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: 100%
Return-value docs: 100%
References docs: 56%

Downloads

2K

CRAN downloads in the past year

Rank #21,793 · ~5/day · ~163/mo

Releases R versions

Daily download trend is not available in this view yet.

13430 days

50390 days

2K1 year

Compare downloads with other packages →

Also on363 r2u16 autocran29 c2d4u

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (1)

R >= 2.15.1

Imports (1)

seqinr

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 (3)

Maintainer (1)

Nora M. Villanueva

Author, Maintainer

Authors (2)

Nora M. Villanueva

Author, Maintainer

Marta Sestelo

Author

Contributors (1)

Alan Miller

Contributor · added in 1.1.0

Listed in earlier versions (1)

Javier Roca-Pardinas

no longer listed · 1.0

Package Timeline

4 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
2.0.1Latest
2024-09-30 · current release · diff ↗
unarchivedReturned to CRAN
2024-09-30
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2023-09-26
check issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
2.0.0
2023-04-20 · diff ↗
1.1.0
2023-01-06 · diff ↗
unarchivedReturned to CRAN
2023-01-06
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21

Show 7 earlier events

R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
archivedRemoved from CRAN
2014-01-01
Fortran 9x errors were not corrected
R
R 3.0.0 released · 2013-04-03
1.0
2012-08-23
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-08-23
Total releases: 4 / 14 yrs
License: GPL
Minimum R: ≥ 2.15.1
Bundled data: 7.8 KB / 1 file
Download size: 36 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("seq2R")

Format

M. Villanueva, N., Miller, A., & Sestelo, M. (2024). seq2R: Simple Method to Detect Compositional Changes in Genomic Sequences (Version 2.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.seq2R

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 seq2R version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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