R Observatory: Metrics for seqmagick version 0.1.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

seqmagick

0.1.8

Sequence Manipulation Utilities

0packages depend

14Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Guangchuang YuFirst published 2019-12-168 releasesCRAN page ↗GitHub ↗

Tools for reading and writing biological sequences in multiple formats, including 'FASTA', 'PHYLIP', 'CLUSTAL', 'STOCKHOLM', 'MEGA' and 'GenBank'. Supports interleaved and sequential layouts where applicable, converts between formats, and manipulates sequence sets (e.g., filtering by patterns and computing consensus sequences from alignments). Also includes functions to download nucleotide records from NCBI by accession.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("seqmagick", 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("YuLab-SMU/seqmagick")

Development version from YuLab-SMU/seqmagick. 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-seqmagick

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

Health

CRAN checks

13OK

Slowest check: 3.2 min · r-release-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

5

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 57%
Documented parameters: 100%
Return-value docs: 100%
References docs: 4%

Downloads

14K

CRAN downloads in the past year

Rank #3,537 · ~38/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

64630 days

2.7K90 days

14K1 year

Compare downloads with other packages →

Also on139 r2u1.1K bioconda

Repository

GitHub ↗ yulab-smu/seqmagick

6Stars

2Forks

0Open issues

0Open PRs

0Releases

62Commits

3Contributors

62 commits · Last activity 2026-01-31

Stars over time

2023-11-14 · 62026-07-07 · 6

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/yulab-smu/seqmagick on 2026-08-23.

Reproducibility and dev environment (1)

Makefile

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (5)

Biostrings magrittrstatsutilsyulab.utils

LinkingTo (0)

none

Suggests (8)

knitr rmarkdown GenomicAlignments GenomicRanges IRanges muscle Rsamtools prettydoc

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Guangchuang Yu

Author, Maintainer

Authors (1)

Guangchuang Yu

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.1.8Latest
2026-01-31 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.1.7
2024-01-09 · diff ↗
0.1.6
2023-06-27 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.1.5
2021-04-25 · diff ↗
0.1.4
2020-09-22 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.3
2019-12-19 · diff ↗
0.1.2
2019-12-18 · diff ↗
0.1.1
2019-12-16
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-12-16
Total releases: 8 / 7 yrs
License: Artistic-2.0 OSI
Minimum R: ≥ 4.1.0
Download size: 163 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("seqmagick")

Format

Yu, G. (2026). seqmagick: Sequence Manipulation Utilities (Version 0.1.8) [Computer software]. https://doi.org/10.32614/CRAN.package.seqmagick

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 seqmagick version 0.1.8 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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