R Observatory: Metrics for GWASinspector version 1.7.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GWASinspector

1.7.4Package record

Comprehensive and Easy to Use Quality Control of GWAS Results

0packages depend

5.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Alireza AniCRAN page ↗

When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.

Changes in 1.7.4

futile.logger package was replaced with logger

From NEWS in the release

Install

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

install.packages("GWASinspector", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-gwasinspector

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-GWASinspector

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-GWASinspector

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: 2.7 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 1.7.4

READMENoVignettesYes · 1 · staticNEWSYes · 67% structured · mentions 1.7.4Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 13includes a package overview page
Examples that run: no examples
Exported functions with examples: 0%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Introduction to GWASinspector HTML

How these are measured

Downloads

5.6K

CRAN downloads in the past year

Rank #11,009 · ~15/day · ~463/mo

Releases R versions

Daily download trend is not available in this view yet.

44830 days

95990 days

5.6K1 year

Compare downloads with other packages →

Also on85 r2u3 autocran

How downloads are counted

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing GWASinspector adds 64 packages (32 with compiled code, 61 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.2

Imports (15)

ini logger data.table hashtoolsggplot2 knitr rmarkdown gridExtragridRSQLite kableExtra (>= 0.8)methodsR.utils openxlsx

LinkingTo (0)

none

Suggests (0)

none

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 (4)

Alireza Ani

Author, Maintainer since 1.1.2 (2019)

Ilja M. Nolte

Author

Ahmad Vaez

Author

Peter J. van der Most

Author

Releases (24)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.7.4Latest
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2026-01-29 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.7.3
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2025-03-30 · diff ↗
1.7.1
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2024-05-06 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.6.5
record
2023-09-27 · diff ↗
1.6.4
record
2023-05-15 · diff ↗ ·
removed 9 exports
setup.inspector, run.inspector, result.inspector, demo.inspector, compare.GWASs, system.check, get.config, get.headerTranslation, manhattan.plot

added 9 exports
setup_inspector, run_inspector, result_inspector, demo_inspector, compare_GWASs, system_check, get_config, get_headerTranslation, manhattan_plot
R
R 4.3.0 released · 2023-04-21
1.6.1
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2023-01-09 · diff ↗
1.6.0
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2022-11-22 · diff ↗
1.5.7.2
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2022-04-27 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.5.7.1
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2022-01-16 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.5.2
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2021-03-22 · diff ↗

Show 16 earlier eventsHide 16 earlier events

1.5.1
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2021-02-08 · diff ↗
1.4.8.2
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2020-10-01 · diff ↗
1.4.8
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2020-07-28 · diff ↗
1.4.7.1
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2020-05-11 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.4.7
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2020-04-22 · diff ↗
1.4.6.7
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2020-03-31 · diff ↗ ·
removed 1 export
sqlite.db.check
1.4.6
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2020-03-23 · diff ↗
1.4.5
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2020-03-15 · diff ↗
1.4.4
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2020-02-25 · diff ↗
1.4.3
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2020-02-18 · diff ↗
1.4.2
record
2020-01-19 · diff ↗ ·
removed 2 exports
sample.inspector, man.plot

added 2 exports
demo.inspector, manhattan.plot
1.3.4
record
2019-12-01 · diff ↗ ·
removed 5 exports
inspect, inspect.example, reformat.columns, check.database, find.variants

added 5 exports
setup.inspector, run.inspector, result.inspector, sample.inspector, sqlite.db.check
1.2
record
2019-09-25 · diff ↗
1.1.2
record
2019-08-02
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-02
Total releases: 24 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.2
Download size: 578 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("GWASinspector")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/bioinformatics/btaa1084.

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 GWASinspector version 1.7.4 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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