seqmagick

0.1.8

Sequence Manipulation Utilities

0packages depend

13.9Kdownloads / 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: 4.2 min · r-devel-linux-x86_64-fedora-gcc

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

README

Dependencies · direct

Check history

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

Downloads

13.9K

CRAN downloads in the past year

Rank #3,476 · ~38/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.1K30 days

3.4K90 days

13.9K1 year

Compare downloads with other packages →

Also on140 r2u1.1K bioconda

Repository

GitHub ↗ yulab-smu/seqmagick

6Stars

2Forks

0Open issues

0Open PRs

0Releases

62Commits

62 commits · 0% stars, 30d

Stars over time

2023-11-14 · 62026-07-07 · 6

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

Code Composition

R 1,305 (60%)Rd 740 (34%)Vignettes 115 (5%)

Code characteristics

Cyclomatic complexity: 2.0 median / 16 max
Documented parameters: 100%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

52 29 exported

Complexity

2.9 avg / 16 max

Call network

52 nodes / 48 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (1)

Maintainer (1)

Guangchuang Yu

Author, Maintainer

Authors (1)

Guangchuang Yu

Author, Maintainer

Release 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