R Observatory: Metrics for GARCOM version 1.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GARCOM

1.2.2Package record

Gene and Region Counting of Mutations ("GARCOM")

0packages depend

2.6Kdownloads / year

54.2%test coverage

11/13flavors OK

Overview

About

Maintained by Sanjeev SariyaCRAN page ↗

Gene and Region Counting of Mutations (GARCOM) package computes mutation (or alleles) counts per gene per individuals based on gene annotation or genomic base pair boundaries. It comes with features to accept data formats in plink(.raw) and VCF. It provides users flexibility to extract and filter individuals, mutations and genes of interest.

Changes in 1.2.2

Date Dec 19 2022
Added about VCF sample

From NEWS.md in the release

Install

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

install.packages("GARCOM", 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-garcom

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-GARCOM

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Sanjeev Sariya <sanjeevsariya@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 2.0 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.2

READMEYes · 97 wordsVignettesNoNEWSYes · 100% structured · mentions 1.2.2Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 9
Examples that run: 50%2 run in a plain check · 2 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #16,649 · ~7/day · ~219/mo

Releases R versions

Daily download trend is not available in this view yet.

26530 days

76190 days

2.6K1 year

Compare downloads with other packages →

Also on66 r2u

How downloads are counted

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing GARCOM adds 27 packages (17 with compiled code, 34 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, pinfsc50 3.3 MB.

Depends (1)

R >= 3.5.0

Imports (3)

data.tablestatsvcfR

LinkingTo (0)

none

Suggests (1)

testthat

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 (2)

Sanjeev Sariya

Giuseppe Tosto

Author, Copyright holder

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.2.2Latest
record
2022-12-23 · current release · diff ↗
1.2.1
record
2022-12-14 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.2.0
record
2020-10-16
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-10-16
Total releases: 3 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 10 KB / 5 files
Download size: 26 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("GARCOM")

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

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 GARCOM version 1.2.2 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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