R Observatory: Metrics for seqminer version 9.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

seqminer

9.9

Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

0packages depend

11.3Kdownloads / year

40.5%test coverage

11/13checks pass

Overview

About

Maintained by Xiaowei ZhanFirst published 2013-03-2043 releasesCRAN page ↗GitHub ↗

Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read 'RareMETAL' summary statistics files; (3) read tables from a 'tabix'-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.

Install

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

install.packages("seqminer", 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("zhanxw/seqminer")

Development version from zhanxw/seqminer. 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-seqminer

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-seqminer

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-seqminer

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

Health

CRAN checks

2WARNING11OK

Failing flavors

WARNING r-oldrel-macos-x86_64
WARNING r-release-macos-x86_64

Slowest check: 7.4 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.22

40.5%

Coverage · measured lines

100%

Documentation · exports

0

Dependencies · direct

Check history

WARNING2026-06-09
11 OK · 0 NOTE · 2 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
10 OK · 0 NOTE · 2 WARNING · 1 ERROR · 0 FAILURE
WARNING2026-03-10
10 OK · 2 NOTE · 2 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 346 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 97%
Documented parameters: 100%
Return-value docs: 80%
References docs: 0%

Downloads

11.3K

CRAN downloads in the past year

Rank #3,982 · ~31/day · ~939/mo

Releases R versions

Daily download trend is not available in this view yet.

49130 days

2.1K90 days

11.3K1 year

Compare downloads with other packages →

Also on496 r2u33 autocran6.3K conda_forge713 bioconda

Repository

GitHub ↗ zhanxw/seqminer

34Stars

12Forks

18Open issues

0Open PRs

1Releases

224Commits

9Contributors

sequencingannotationnext-generation-sequencingmeta-analysisvcfbcftabixbgen

224 commits · Last activity 2026-02-23 · +3% stars, 30d

Stars over time

2025-08-22 · 312026-08-20 · 34

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/zhanxw/seqminer on 2026-08-23.

Continuous integration (2)

GitHub ActionsAppVeyor

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

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (0)

none

LinkingTo (0)

none

Suggests (2)

testthat SKAT

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (7)

Maintainer (1)

Xiaowei Zhan

Author, Maintainer

Authors (2)

Xiaowei Zhan

Author, Maintainer

Dajiang Liu

Author

Copyright holders (5)

Attractive Chaos

Copyright holder · added in 5.3

Broad Institute / Massachusetts Institute of Technology

Copyright holder · added in 5.3

D. Richard Hipp

Copyright holder · added in 8.4

Facebook, Inc

Copyright holder · added in 6.7

Genome Research Ltd (GRL)

Copyright holder · added in 5.3

Listed in earlier versions (10)

with contributions of Jean-loup Gailly

no longer listed · 0.1 to 3.1

Julian Seward (this author wrote bzip2

no longer listed · 0.1 to 3.1

provide license so we include zlib source code)

no longer listed · 0.1 to 3.1

with BSD license we include bzip2 source codes)

no longer listed · 0.1 to 3.1

with MIT license we include tabix source codes).

no longer listed · 0.1 to 5.2

Heng Li (this author wrote tabix

no longer listed · 0.1 to 3.1

Mark Adler(they wrote zlib

no longer listed · 0.1 to 2.2

Mark Adler (they wrote zlib

no longer listed · 2.7 to 3.1

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
9.9Latest
2026-02-24 · current release · diff ↗
unarchivedReturned to CRAN
2026-02-24
archivedRemoved from CRAN
2026-01-29
issues were not corrected in time
R
R 4.5.0 released · 2025-04-11
9.7
2024-10-02 · diff ↗
R
R 4.4.0 released · 2024-04-24
9.4
2024-02-03 · diff ↗
9.3
2023-11-28 · diff ↗
9.1
2023-09-02 · diff ↗
R
R 4.3.0 released · 2023-04-21
8.9
2023-04-07 · diff ↗
8.6
2023-01-26 · diff ↗
8.5
2022-11-15 · diff ↗
R
R 4.2.0 released · 2022-04-22
8.4
2022-02-07 · diff ↗

Show 44 earlier events

8.2
2021-11-09 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
8.0
2020-03-02 · diff ↗
R
R 3.6.0 released · 2019-04-26
7.1
2019-01-08 · diff ↗
7.0
2019-01-07 · diff ↗
6.7
2018-12-06 · diff ↗
6.1
2018-08-02 · diff ↗
R
R 3.5.0 released · 2018-04-23
6.0
2017-05-05 · diff ↗
R
R 3.4.0 released · 2017-04-21
5.9
2017-04-18 · diff ↗
5.7
2017-01-13 · diff ↗
5.3
2016-05-07 · diff ↗
5.2
2016-05-03 · diff ↗
R
R 3.3.0 released · 2016-05-03
5.0
2015-10-22 · diff ↗
4.9
2015-09-16 · diff ↗
4.7
2015-08-19 · diff ↗
4.5
2015-06-29 · diff ↗
4.2
2015-06-10 · diff ↗
3.9
2015-05-21 · diff ↗
3.7
2015-05-16 · diff ↗
R
R 3.2.0 released · 2015-04-16
3.4
2014-12-08 · diff ↗
3.1
2014-05-07 · diff ↗
3.0
2014-04-19 · diff ↗
2.7
2014-04-14 · diff ↗
R
R 3.1.0 released · 2014-04-10
2.2
2014-01-27 · diff ↗
2.0
2013-11-20 · diff ↗
1.9.1
2013-11-15 · diff ↗
1.9
2013-11-11 · diff ↗
1.4
2013-09-29 · diff ↗
1.3
2013-09-26 · diff ↗
1.0
2013-09-04 · diff ↗
0.7
2013-07-29 · diff ↗
0.5
2013-05-28 · diff ↗
0.3
2013-04-13 · diff ↗
R
R 3.0.0 released · 2013-04-03
0.2
2013-04-01 · diff ↗
0.1
2013-03-20
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2013-03-20
Total releases: 43 / 13 yrs
License: GPL | file LICENSE
Download size: 4.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("seqminer")

Format

Zhan, X., Attractive Chaos, Broad Institute / Massachusetts Institute of Technology, D. Richard Hipp, Facebook, Inc, Genome Research Ltd (GRL), & Liu, D. (2026). seqminer: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R (Version 9.9) [Computer software]. https://doi.org/10.32614/CRAN.package.seqminer

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 seqminer version 9.9 [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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