R Observatory: Metrics for baseq version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

baseq

0.2.0Package record

Basic Sequence Processing Tool for Biological Data

0packages depend

3.6Kdownloads / year

47.0%test coverage

13/13flavors OK

Overview

About

Maintained by Ambu VijayanCRAN page ↗GitHub ↗Issues ↗

Primarily created as an easy and understanding way to do basic sequences surrounding the central dogma of molecular biology.

Changes in 0.2.0

Replaced slow loops with highly optimized, vectorized functions for sequence translation, cleaning, and file reading.
Introduced universal wrappers (clean_seq, read_seq, write_seq, rev_comp) to simplify workflows, along with snake_case aliases (clean_dna_seq, clean_rna_seq) while maintaining backward compatibility.
Added find_longest_orf, find_cpg_islands, search_motif, shuffle_sequence, and robust sequence simulators (simulate_sequence, simulate_fasta, simulate_fastq).
Added calculate_tm, calculate_mw, calculate_pi, calculate_charge, and simulate_pcr, simulate_digestion.
Added publication-ready ggplot2 functions (plot_gc_skew, plot_hydrophobicity, plot_aa_composition, plot_dotplot).
Added baseq_dna and baseq_rna object classes and translate() S3 method. Added as_Biostrings bridge.
Added a comprehensive testthat suite with 30+ passing categories handling edge cases (NA/NULL handling, blank inputs, malformed files).

From NEWS.md in the release

Install

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

install.packages("baseq", 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("ambuvjyn/baseq")

Development version from ambuvjyn/baseq. 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-baseq

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-baseq

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-baseq

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: 1.4 min · r-oldrel-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 0.2.0

READMEYes · 295 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.2.0Citation fileNo

Help pages: 43
Examples that run: 92%11 run in a plain check · 1 hold no code
Exported functions with examples: 29%
Documented parameters: 100%
Return-value docs: 98%
Help pages citing references: 0%

Vignettes (1)

Introduction to baseq HTML

How these are measured

Downloads

3.6K

CRAN downloads in the past year

Rank #12,054 · ~10/day · ~298/mo

Releases R versions

Daily download trend is not available in this view yet.

33630 days

91890 days

3.6K1 year

Compare downloads with other packages →

Also on105 r2u22 autocran

How downloads are counted

Repository

ambuvjyn/baseq ↗Account: ambuvjyn

4Stars

0Forks

0Open issues

0Open PRs

6Releases

27Commits

1Commit identities

bioinformaticsrsequencing

27 commits · Last activity 2026-03-11 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-04-16 · 32026-07-07 · 4

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/ambuvjyn/baseq on 2026-10-21.

Docs source (2)

pkgdown

GitHub Pages site last deployed 2023-04-27

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing baseq adds 17 packages (7 with compiled code, 14 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

Depends (1)

R >= 3.5.0

Imports (1)

ggplot2

LinkingTo (0)

none

Suggests (4)

testthat rmarkdown knitr Biostrings

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 (2)

Ambu Vijayan

Author, Maintainer since 0.1.0 (2023)

J. Sreekumar

Author · added in 0.1.1

Principal Scientist, ICAR - Central Tuber Crops Research Institute

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.2.0Latest
record
2026-03-11 · current release · diff ↗ ·
removed 19 exports
clean_DNA_file, clean_DNA_sequence, clean_RNA_file, clean_RNA_sequence, clean_sequence, count_seq_pattern, gc_content_file, read.fasta_to_df, read.fasta_to_list, read.fastq_to_df, read.fastq_to_list, reverse_complement, rna_reverse_complement, write.df_to_fasta, write.df_to_fastq, write.dna_to_rna, write.list_to_fasta, write.list_to_fastq, write.rna_to_dna

added 35 exports
as_Biostrings, as_baseq_dna, as_baseq_rna, calculate_assembly_stats, calculate_charge, calculate_codon_usage, calculate_identity, calculate_mw, calculate_pi, calculate_tm, clean_file, clean_seq, count_kmers, count_pattern, filter_fastq_quality, find_cpg_islands, find_longest_orf, get_genetic_code, plot_aa_composition, plot_dotplot, plot_gc_skew, plot_hydrophobicity, read_seq, rev_comp, reverse_translate, search_motif, shuffle_sequence, simulate_digestion, simulate_fasta, simulate_fastq and 5 more
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.1.4
record
2023-05-03 · diff ↗
0.1.2
record
2023-04-28 · diff ↗ ·
added 2 exports
write.dna_to_rna, write.rna_to_dna
0.1.1
record
2023-04-26 · diff ↗ ·
removed 1 export
read.fasta

added 14 exports
clean_DNA_file, clean_DNA_sequence, clean_RNA_file, clean_RNA_sequence, fastq_to_fasta, gc_content_file, read.fasta_to_df, read.fasta_to_list, read.fastq_to_df, read.fastq_to_list, write.df_to_fasta, write.df_to_fastq, write.list_to_fasta, write.list_to_fastq
R
R 4.3.0 released · 2023-04-21
0.1.0
record
2023-03-22
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-03-22
Total releases: 5 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 0.4 KB / 1 file
Download size: 48 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("baseq")

Format

Vijayan, A., & Sreekumar, J. (2026). baseq: Basic Sequence Processing Tool for Biological Data (Version 0.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.baseq

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 baseq version 0.2.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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