R Observatory: Metrics for seq2R version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

seq2R

2.0.1Package record

Simple Method to Detect Compositional Changes in Genomic Sequences

0packages depend

2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Nora M. VillanuevaCRAN 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. 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-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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.4 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.1

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9includes a package overview page
Examples that run: 100%8 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 56%

Also includes 2 demo scripts (run with demo())

How these are measured

Downloads

2K

CRAN downloads in the past year

Rank #24,178 · ~6/day · ~169/mo

Releases R versions

Daily download trend is not available in this view yet.

18330 days

52490 days

2K1 year

Compare downloads with other packages →

Also on331 r2u3 autocran20 c2d4u

How downloads are counted

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Installing seq2R adds 7 packages (5 with compiled code, 14 MB of source tarballs). Heaviest: sp 4.3 MB, seqinr 3.4 MB, ade4 3.2 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Nora M. Villanueva

Author, Maintainer since 1.0 (2012)

Marta Sestelo

Author

Alan Miller

Contributor · added in 1.1.0

FORTRAN code lsq.f90: weighted least-squares module

Listed in earlier versions (1)

Javier Roca-Pardinas

no longer listed · 1.0

Releases (4)

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
2024-09-30
2.0.1Latest
record
2024-09-30 · current release · diff ↗
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
record
2023-04-20 · diff ↗ ·
removed 2 exports
change.binary, change.points

added 2 exports
transform, find.points
unarchivedReturned to CRAN
2023-01-06
1.1.0
record
2023-01-06 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 7 exports
change.binary, change.points, critical, plot.change.points, print.change.points, read.all, read.genbank
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 eventsHide 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
record
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

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 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 seq2R version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →