SkeletalVis

0.1.2

Exploration and Visualisation of Skeletal Transcriptomics Data

0packages depend

3.9Kdownloads / year

79.8%test coverage

12/13checks pass

Overview

About

Maintained by Jamie SoulFirst published 2025-05-062 releasesCRAN page ↗GitHub ↗

Allows search and visualisation of a collection of uniformly processed skeletal transcriptomic datasets. Includes methods to identify datasets where genes of interest are differentially expressed and find datasets with a similar gene expression pattern to a query dataset Soul J, Hardingham TE, Boot-Handford RP, Schwartz JM (2019) doi:10.1093/bioinformatics/bty947.

Install

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

install.packages("SkeletalVis", 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("soulj/SkeletalVis")

Development version from soulj/SkeletalVis. 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-skeletalvis

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-SkeletalVis

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-SkeletalVis

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.68

79.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 148 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

3.9K

CRAN downloads in the past year

Rank #19,324 · ~11/day · ~329/mo

Releases R versions

Daily download trend is not available in this view yet.

16230 days

56790 days

3.9K1 year

Compare downloads with other packages →

Also on130 r2u5 autocran

Repository

GitHub ↗ soulj/skeletalvis

0Stars

0Forks

0Open issues

0Open PRs

0Releases

gene-expressionosteoarthritisrpackage

Last activity 2025-12-19

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/soulj/skeletalvis on 2026-08-02.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (17)

arrow cowplot dplyr DT ggplot2 ggrepel httr igraph miniUI pbapply plotly rlang shinystatstidyrutilsvisNetwork

LinkingTo (0)

none

Suggests (5)

mockery rmarkdown knitr testthat withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Jamie Soul

Author, Maintainer, Copyright holder

Authors (1)

Jamie Soul

Author, Maintainer, Copyright holder

Jamie Soul

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.1.2Latest
2025-12-19 · current release · diff ↗
0.1.1
2025-05-06
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-06
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0
Bundled data: 345 KB / 1 file
Download size: 1.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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