R Observatory: Metrics for scDHA version 1.2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scDHA

1.2.3

Single-Cell Decomposition using Hierarchical Autoencoder

0packages depend

2.9Kdownloads / year

57.1%test coverage

13/13checks pass

Overview

About

Maintained by Ha NguyenFirst published 2021-06-097 releasesCRAN page ↗GitHub ↗

Provides a fast and accurate pipeline for single-cell analyses. The 'scDHA' software package can perform clustering, dimension reduction and visualization, classification, and time-trajectory inference on single-cell data (Tran et.al. (2021) DOI:10.1038/s41467-021-21312-2).

Install

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

install.packages("scDHA", 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("duct317/scDHA")

Development version from duct317/scDHA. 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-scdha

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-scDHA

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-scDHA

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

Health

CRAN checks

13OK

Slowest check: 4.6 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.03

57.1%

Coverage · measured lines

100%

Documentation · exports

14

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 3 earlier snapshots

NOTE2026-04-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 355 wordsVignettesYes · staticpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

2.9K

CRAN downloads in the past year

Rank #11,522 · ~8/day · ~240/mo

Releases R versions

Daily download trend is not available in this view yet.

27330 days

85590 days

2.9K1 year

Compare downloads with other packages →

Also on518 r2u20 autocran

Repository

GitHub ↗ duct317/scdha

42Stars

6Forks

3Open issues

0Open PRs

2Releases

63Commits

5Contributors

63 commits · Last activity 2025-09-24 · 0% stars, 30d

Stars over time

2025-06-11 · 412026-07-07 · 42

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/duct317/scdha on 2026-08-16.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4

Imports (14)

matrixStats foreach doParallel igraphMatrixuwotclusterRcpp RcppParallel RcppAnnoymethodstorch (>= 0.3.0)RhpcBLASctl coro

LinkingTo (4)

Rcpp RcppArmadillo RcppParallel RcppAnnoy

Suggests (3)

testthat knitr mclust

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Ha Nguyen

Maintainer · added in 1.2.2

Authors (1)

Duc Tran

Author

Contributors (1)

Hao Chen

Contributor · added in 1.2.1

Funders (1)

Tin Nguyen

Funder

Listed in earlier versions (2)

Klaus Schliep

no longer listed · 1.2.1

Shibiao Wan

no longer listed · 1.2.1

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.2.3Latest
2025-09-24 · current release · diff ↗
unarchivedReturned to CRAN
2025-09-24
R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2025-03-14
issues were not corrected in time
R
R 4.4.0 released · 2024-04-24
1.2.2
2024-04-03 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.1
2023-04-04 · diff ↗
unarchivedReturned to CRAN
2023-04-04
archivedRemoved from CRAN
2023-03-11
requires archived package 'clusterCrit'
1.2.0
2022-08-18 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.2
2021-09-15 · diff ↗
1.1.1
2021-06-11 · diff ↗
1.1.0
2021-06-09

Show 1 earlier events

R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-06-09
Total releases: 7 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.4
Bundled data: 2.2 MB / 2 files
Download size: 2.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scDHA")

Format

Nguyen, H., Chen, H., Nguyen, T., & Tran, D. (2025). scDHA: Single-Cell Decomposition using Hierarchical Autoencoder (Version 1.2.3) [Computer software]. https://doi.org/10.32614/CRAN.package.scDHA

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 scDHA version 1.2.3 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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