R Observatory: Metrics for HodgesTools version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HodgesTools

1.0.0Package record

Common Use Tools for Genomic Analysis

0packages depend

2.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Tyler HansenCRAN page ↗Declared funder: Emily Hodges

Built by Hodges lab members for current and future Hodges lab members. Other individuals are welcome to use as well. Provides useful functions that the lab uses everyday to analyze various genomic datasets. Critically, only general use functions are provided; functions specific to a given technique are reserved for a separate package. As the lab grows, we expect to continue adding functions to the package to build on previous lab members code.

Changes in 1.0.0

Added a NEWS.md file to track changes to the package.
Initial release of HodgesTools

From NEWS.md in the release

Install

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

install.packages("HodgesTools", 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-hodgestools

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-HodgesTools

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-HodgesTools

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: 1.4 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 1.0.0

READMEYes · 178 wordsVignettesNoNEWSYes · 67% structured · mentions 1.0.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 8
Examples that run: 100%4 run in a plain check
Exported functions with examples: 80%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #17,923 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

25430 days

71990 days

2.9K1 year

Compare downloads with other packages →

Also on66 r2u

How downloads are counted

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing HodgesTools adds 66 packages (31 with compiled code, 41 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, RSQLite 4.2 MB.

Depends (1)

R >= 3.6

Imports (9)

dplyr ggplot2 magrittr RColorBrewer readr ini qqman data.table RecordLinkage

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 (5)

Tyler Hansen

Verda Agan

Author, Contributor, Copyright holder

Lindsey Guerin

Author, Contributor, Copyright holder

Emily Hodges

Author, Funder, Copyright holder

Tim Scott

Author, Contributor, Copyright holder

Releases (1)

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
1.0.0Latest
record
2022-12-08 · current release
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-12-08
Total releases: 1 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.6
Download size: 357 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HodgesTools")

Format

Hansen, T., Agan, V., Guerin, L., Hodges, E., & Scott, T. (2022). HodgesTools: Common Use Tools for Genomic Analysis (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.HodgesTools

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 HodgesTools version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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