R Observatory: Metrics for chromseq version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

chromseq

0.1.3

Split Chromosome 'Fasta' File

0packages depend

2.4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Shaoqian MaFirst published 2020-05-111 releasesCRAN page ↗GitHub ↗

Chromosome files in the 'Fasta' format usually contain large sequences like human genome. Sometimes users have to split these chromosomes into different files according to their chromosome number. The 'chromseq' can help to handle this. So the selected chromosome sequence can be used for downstream analysis like motif finding. Howard Y. Chang(2019) doi:10.1038/s41587-019-0206-z.

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("MSQ-123/chromseq")

Development version from MSQ-123/chromseq. Installs pak first if it is not already available.

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-chromseq

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-chromseq

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-chromseq

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 52 s · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

2

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 135 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 38%

Downloads

2.4K

CRAN downloads in the past year

Rank #21,521 · ~7/day · ~201/mo

Releases R versions

Daily download trend is not available in this view yet.

12030 days

50990 days

2.4K1 year

Compare downloads with other packages →

Also on119 r2u9 autocran

Repository

GitHub ↗ msq-123/chromseq

4Stars

0Forks

0Open issues

0Open PRs

0Releases

8Commits

1Contributors

8 commits · Last activity 2020-05-19

Stars over time

2023-01-03 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/msq-123/chromseq on 2026-08-16.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (2)

utilsbase

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Shaoqian Ma

Author, Maintainer

Authors (1)

Shaoqian Ma

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.3Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2020-05-11
Total releases: 1 / 6 yrs
License: Artistic-2.0 OSI
Minimum R: ≥ 2.10
Bundled data: 52 KB / 3 files
Download size: 58 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("chromseq")

Format

Ma, S. (2020). chromseq: Split Chromosome 'Fasta' File (Version 0.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.chromseq

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 chromseq version 0.1.3 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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