R Observatory: Metrics for scINSIGHT version 0.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scINSIGHT

0.1.5Package record

Interpretation of Heterogeneous Single-Cell Gene Expression Data

0packages depend

2.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Kun QianCRAN page ↗GitHub ↗Website ↗

We develop a novel matrix factorization tool named 'scINSIGHT' to jointly analyze multiple single-cell gene expression samples from biologically heterogeneous sources, such as different disease phases, treatment groups, or developmental stages. Given multiple gene expression samples from different biological conditions, 'scINSIGHT' simultaneously identifies common and condition-specific gene modules and quantify their expression levels in each sample in a lower-dimensional space. With the factorized results, the inferred expression levels and memberships of common gene modules can be used to cluster cells and detect cell identities, and the condition-specific gene modules can help compare functional differences in transcriptomes from distinct conditions. Please also see Qian K, Fu SW, Li HW, Li WV (2022) doi:10.1186/s13059-022-02649-3.

Install

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

install.packages("scINSIGHT", 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("Vivianstats/scINSIGHT")

Development version from Vivianstats/scINSIGHT. 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-scinsight

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-scINSIGHT

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-scINSIGHT

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: 3.3 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
WARNING12 OK, 1 WARNING2026-06-08
OK13 OK2026-05-02

Show 6 earlier changesHide 6 earlier changes

NOTE11 OK, 1 NOTE2026-04-25
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-04-16
NOTE13 OK, 1 NOTE2026-03-28
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.5

READMEYes · 183 wordsVignettesNoNEWSNoCitation fileNoWebsiteYes

Help pages: 3
Examples that run: 100%1 run in a plain check
Exported functions with examples: 50%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #14,251 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

27530 days

83690 days

2.9K1 year

Compare downloads with other packages →

Also on381 r2u3 autocran51 c2d4u

How downloads are counted

Repository

vivianstats/scinsight ↗Account: Vivianstats

22Stars

3Forks

8Open issues

0Open PRs

0Releases

11Commits

2Commit identities

scrna-seqintegrationgene-expressionbioinformatics

11 commits · Last activity 2022-05-29 · 0% stars, 30d · The default branch showed an older version (0.1.4) than CRAN on 2026-10-21

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-08-14 · 212026-07-11 · 22

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/vivianstats/scinsight on 2026-10-21.

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing scINSIGHT adds 14 packages (10 with compiled code, 22 MB of source tarballs). Heaviest: stringi 11 MB, igraph 4.8 MB, Rcpp 1.8 MB.

Depends (1)

methods

Imports (6)

Rcpp RANN igraphparallelstatsstringr

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Kun Qian

Author, Contributor, Maintainer since 0.1.0 (2021)

Wei Vivian Li

Author, Contributor

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.1.5Latest
record
2025-10-18 · current release · diff ↗
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
0.1.4
record
2022-05-30 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.1.3
record
2022-02-03 · diff ↗
0.1.2
record
2022-01-24 · diff ↗
0.1.1
record
2021-09-06 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.0
record
2021-05-03
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-05-03
Total releases: 6 / 5 yrs
License: GPL-3 OSI
Download size: 15 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scINSIGHT")

Format

Qian, K., & Li, W. V. (2025). scINSIGHT: Interpretation of Heterogeneous Single-Cell Gene Expression Data (Version 0.1.5) [Computer software]. https://doi.org/10.32614/CRAN.package.scINSIGHT

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 scINSIGHT version 0.1.5 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →