R Observatory: Metrics for hidecan version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hidecan

1.1.0Package record

Create HIDECAN Plots for Visualising Genome-Wide Association Studies and Differential Expression Results

1packages depend

3.1Kdownloads / year

75.2%test coverage

0/13flavors OK

Overview

About

Maintained by Olivia Angelin-BonnetCRAN page ↗GitHub ↗Website ↗Issues ↗

Generates HIDECAN plots that summarise and combine the results of genome-wide association studies (GWAS) and transcriptomics differential expression analyses (DE), along with manually curated candidate genes of interest. The HIDECAN plot is presented in Angelin-Bonnet et al. (2023) (currently in review).

Changes in 1.1.0

Removed get_gwaspoly_example_data() function so that the package doesn't depend on GWASpoly (for CRAN submission)
Saved the example object previously returned by get_gwaspoly_example_data() in as an rda file in the extdata folder

From NEWS.md in the release

Install

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

install.packages("hidecan", 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("PlantandFoodResearch/hidecan")

Development version from PlantandFoodResearch/hidecan. 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-hidecan

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-hidecan

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-hidecan

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

13NOTE

Check messages

NOTEDESCRIPTION meta-informationr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘apply_threshold.R’ ‘compute_chromosomes_length.R’
    ‘create_hidecan_plot.R’ ‘gwaspoly_helper_functions.R’
    ‘input_data_constructors.R’

r-devel-windows-x86_64, r-oldrel-windows-x86_64, r-release-windows-x86_64

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'apply_threshold.R' 'compute_chromosomes_length.R'
    'create_hidecan_plot.R' 'gwaspoly_helper_functions.R'
    'input_data_constructors.R'

CRAN check page ↗

Slowest check: 2.6 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE3 OK, 11 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMEYes · 215 wordsVignettesYes · 2 · dynamicNEWSYes · 67% structured · mentions 1.1.0Citation fileNoWebsiteYes · pkgdown

Help pages: 20
Examples that run: 100%8 run in a plain check (2 of them under a condition)
Exported functions with examples: 62%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

hidecan HTML
hidecan-step-by-step HTML

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #11,131 · ~9/day · ~262/mo

Releases R versions

Daily download trend is not available in this view yet.

35330 days

95390 days

3.1K1 year

Compare downloads with other packages →

Also on91 r2u2 autocran

How downloads are counted

Repository

plantandfoodresearch/hidecan ↗Organization: PlantandFoodResearch

8Stars

1Forks

0Open issues

0Open PRs

1Releases

99Commits

1Commit identities

99 commits · Last activity 2025-07-17 · 0% stars, 30d · Default branch at 1.2.0.0, ahead of CRAN 1.1.0 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-03-19 · 72026-08-05 · 8

How these are measured

PracticesBeta

10 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/plantandfoodresearch/hidecan on 2026-10-21.

Continuous integration (1)

GitHub Actions

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-07-17 · The repository has a site deploy workflow

pkgdown site last built 2025-07-17

Reproducibility and dev environment (2)

renvdata-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing hidecan adds 64 packages (35 with compiled code, 57 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (1)

R >= 3.5.0

Imports (10)

dplyr ggnewscale ggplot2 ggrepel purrr shiny tibble tidyr viridis vroom

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown stringr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

viewpoly

How these are counted

Code & Tests

Datasets

People & History

People (1)

Olivia Angelin-Bonnet

Author, Maintainer since 1.1.0 (2023)

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
1.1.0Latest
record
2023-02-10 · current release
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-02-10
Total releases: 1 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Download size: 3.2 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hidecan")

Format

Angelin-Bonnet, O. (2023). hidecan: Create HIDECAN Plots for Visualising Genome-Wide Association Studies and Differential Expression Results (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.hidecan

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 hidecan version 1.1.0 [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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