R Observatory: Metrics for SparseDC version 0.1.17

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SparseDC

0.1.17Package record

Implementation of SparseDC Algorithm

0packages depend

5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Jun LiCRAN page ↗

Implements the algorithm described in Barron, M., Zhang, S. and Li, J. 2017, "A sparse differential clustering algorithm for tracing cell type changes via single-cell RNA-sequencing data", Nucleic Acids Research, gkx1113, doi:10.1093/nar/gkx1113. This algorithm clusters samples from two different populations, links the clusters across the conditions and identifies marker genes for these changes. The package was designed for scRNA-Seq data but is also applicable to many other data types, just replace cells with samples and genes with variables. The package also contains functions for estimating the parameters for SparseDC as outlined in the paper. We recommend that users further select their marker genes using the magnitude of the cluster centers.

Install

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

install.packages("SparseDC", 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-sparsedc

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-SparseDC

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-SparseDC

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: 2.5 min · r-release-macos-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
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 0.1.17

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 13
Examples that run: 100%6 run in a plain check
Exported functions with examples: 60%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 0%

Vignettes (1)

sparseDC HTML

How these are measured

Downloads

5K

CRAN downloads in the past year

Rank #14,075 · ~14/day · ~416/mo

Releases R versions

Daily download trend is not available in this view yet.

28630 days

83790 days

5K1 year

Compare downloads with other packages →

Also on134 r2u6 autocran

How downloads are counted

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing SparseDC adds no packages beyond those that come with R.

Depends (1)

R >= 3.1.0

Imports (1)

stats

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

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 (2)

Jun Li

Author, Maintainer since 0.1.5 (2017)

Martin Barron

Author

Releases (4)

Pick two releases to compare their code metrics.

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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.1.17Latest
record
2018-01-04 · current release · diff ↗
0.1.14
record
2017-10-19 · diff ↗
0.1.12
record
2017-09-17 · diff ↗
0.1.5
record
2017-05-02
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-05-02
Total releases: 4 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.0
Bundled data: 4.3 MB / 4 files
Download size: 4.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SparseDC")

Format

Li, J., & Barron, M. (2018). SparseDC: Implementation of SparseDC Algorithm (Version 0.1.17) [Computer software]. https://doi.org/10.32614/CRAN.package.SparseDC

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 SparseDC version 0.1.17 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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