R Observatory: Metrics for seqmagick version 0.1.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

seqmagick

0.1.9Package record

Sequence Manipulation Utilities

0packages depend

14.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Guangchuang YuCRAN page ↗GitHub ↗Issues ↗

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, and reads or writes gzip, bzip2 and xz compressed files transparently. Converts between formats, renames sequences via a two-column mapping, summarizes sequence counts, lengths, GC content and ambiguous characters, 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.

Changes in 0.1.9

fa_summary() to summarize sequences (count, length range, GC content and ambiguous character proportion) (2026-08-27, Thu)
fa_read() and fa_write() support compressed files (.gz, .bz2, .xz) transparently (2026-08-27, Thu)
add testthat test suite covering reading/writing, format conversions, renaming and summaries (2026-08-27, Thu)
remove 'magrittr' dependency, use base pipe (|>) (2026-08-27, Thu)
bs_rename() and fa_rename() default to sep=NULL and position=NULL; unmatched names are kept unchanged (2026-08-27, Thu)
bug fix: keep original names for unmatched entries when both sep and position are set (2026-08-27, Thu)

From NEWS.md in the release

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. 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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE13 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.9

READMEYes · 242 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.1.9Citation fileNo

Help pages: 26 (1 internal)includes a package overview page
Examples that run: 60%9 run in a plain check · 6 never run
Exported functions with examples: 60%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 4%

Vignettes (1)

seqmagick introduction

How these are measured

Downloads

14.2K

CRAN downloads in the past year

Rank #3,502 · ~39/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.2K30 days

3K90 days

14.2K1 year

Compare downloads with other packages →

Also on249 r2u1.3K bioconda

How downloads are counted

Repository

yulab-smu/seqmagick ↗Organization: YuLab-SMU

6Stars

2Forks

0Open issues

0Open PRs

0Releases

65Commits

3Commit identities

65 commits · Last activity 2026-08-29 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 67%
Median days to close, 50 most recently updated closed issues: 808
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2023-11-14 · 62026-07-07 · 6

How these are measured

PracticesBeta

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

Checks run against github.com/yulab-smu/seqmagick on 2026-10-11.

Docs source (2)

README.Rmd

GitHub Pages site last deployed 2017-02-17

Reproducibility and dev environment (1)

Makefile

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing seqmagick adds 6 packages (5 with compiled code, 3.0 MB of source tarballs). Heaviest: fs 1.4 MB, rlang 766 KB, cli 629 KB. 1 more not on CRAN is not measured.

Depends (1)

R >= 4.1.0

Imports (4)

Biostringsstatsutilsyulab.utils

LinkingTo (0)

none

Suggests (9)

knitr rmarkdown testthat GenomicAlignments GenomicRanges IRanges muscle Rsamtools prettydoc

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Guangchuang Yu

Author, Maintainer since 0.1.1 (2019)

Releases (9)

Pick two releases to compare their code metrics.

0.1.9Latest
record
2026-08-30 · current release · diff ↗ ·
added 1 export
fa_summary
R
R 4.6.0 released · 2026-04-24
0.1.8
record
2026-01-31 · diff ↗ ·
added 1 export
ncbi_fa_read
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.1.7
record
2024-01-09 · diff ↗ ·
added 3 exports
clw_read, mega_read, sth_read
0.1.6
record
2023-06-27 · diff ↗ ·
added 1 export
gb_read
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
record
2021-04-25 · diff ↗
0.1.4
record
2020-09-22 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.3
record
2019-12-19 · diff ↗
0.1.2
record
2019-12-18 · diff ↗
0.1.1
record
2019-12-16

Show 1 earlier eventHide 1 earlier event

R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-12-16
Total releases: 9 / 7 yrs
License: Artistic-2.0 OSI
Minimum R: ≥ 4.1.0
Download size: 172 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("seqmagick")

Format

Yu, G. (2026). seqmagick: Sequence Manipulation Utilities (Version 0.1.9) [Computer software]. https://doi.org/10.32614/CRAN.package.seqmagick

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 seqmagick version 0.1.9 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, 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 →