R Observatory: Metrics for TopDom version 0.10.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TopDom

0.10.1

An Efficient and Deterministic Method for Identifying Topological Domains in Genomes

1packages depend

3.2Kdownloads / year

47.1%test coverage

0/13checks pass

Overview

About

Maintained by Henrik BengtssonFirst published 2021-05-061 releasesCRAN page ↗GitHub ↗

The 'TopDom' method identifies topological domains in genomes from Hi-C sequence data (Shin et al., 2016 doi:10.1093/nar/gkv1505). The authors published an implementation of their method as an R script (two different versions; also available in this package). This package originates from those original 'TopDom' R scripts and provides help pages adopted from the original 'TopDom' PDF documentation. It also provides a small number of bug fixes to the original code.

Install

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

install.packages("TopDom", 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("HenrikBengtsson/TopDom")

Development version from HenrikBengtsson/TopDom. 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-topdom

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-TopDom

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-TopDom

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

Health

CRAN checks

13NOTE

Failing flavors

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

Slowest check: 2.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.06

47.1%

Coverage · measured lines

100%

Documentation · exports

5

Dependencies · direct

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 610 wordsVignettesNopkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 67%
Return-value docs: 100%
References docs: 27%

Downloads

3.2K

CRAN downloads in the past year

Rank #12,940 · ~9/day · ~264/mo

Releases R versions

Daily download trend is not available in this view yet.

17830 days

77790 days

3.2K1 year

Compare downloads with other packages →

Also on195 r2u28 autocran

Repository

GitHub ↗ henrikbengtsson/topdom

23Stars

6Forks

8Open issues

1Open PRs

0Releases

255Commits

1Contributors

rpackagehicgenomicscrantopological-domains

255 commits · Last activity 2023-05-11 · 0% stars, 30d

Stars over time

2025-02-21 · 212026-07-07 · 23

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/henrikbengtsson/topdom on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.3.0

Imports (5)

matrixStatsgridggplot2 reshape2 tibble

LinkingTo (0)

none

Suggests (1)

diffobj

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

rnaCrosslinkOO

Code & Tests

People & History

People (5)

Maintainer (1)

Henrik Bengtsson

Author, Maintainer, Copyright holder

Authors (2)

Henrik Bengtsson

Author, Maintainer, Copyright holder

Hanjun Shin

Author, Contractor, Copyright holder

Copyright holders (4)

Henrik Bengtsson

Author, Maintainer, Copyright holder

Hanjun Shin

Author, Contractor, Copyright holder

Gangqing Hu

Contractor, Copyright holder

Harris Lazaris

Contractor, Copyright holder

Other (1)

Xianghong Zhou

Contractor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.10.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2021-05-06
Total releases: 1 / 5 yrs
License: GPL
Minimum R: ≥ 3.3.0
Download size: 4.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TopDom")

Format

Bengtsson, H., Hu, G., Lazaris, H., Shin, H., & Zhou, X. (2021). TopDom: An Efficient and Deterministic Method for Identifying Topological Domains in Genomes (Version 0.10.1) [Computer software]. https://doi.org/10.32614/CRAN.package.TopDom

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 TopDom version 0.10.1 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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