R Observatory: Metrics for scROSHI version 1.0.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scROSHI

1.0.0.1Package record

Robust Supervised Hierarchical Identification of Single Cells

0packages depend

2.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Dominik BurriCRAN page ↗

Identifying cell types based on expression profiles is a pillar of single cell analysis. 'scROSHI' identifies cell types based on expression profiles of single cell analysis by utilizing previously obtained cell type specific gene sets. It takes into account the hierarchical nature of cell type relationship and does not require training or annotated data. A detailed description of the method can be found at: Michael Prummer, Anne Bertolini, Lars Bosshard, Florian Barkmann, Josephine Yates, Valentina Boeva, The Tumor Profiler Consortium , Daniel Stekhoven, Franziska Singer, scROSHI: robust supervised hierarchical identification of single cells, NAR Genomics and Bioinformatics, Volume 5, Issue 2, June 2023, lqad058, doi:10.1093/nargab/lqad058.

Install

R (CRAN)Ubuntu (r2u)

install.packages("scROSHI", 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-scroshi

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10

Show 4 earlier changesHide 4 earlier changes

ERROR12 OK, 1 ERROR2026-05-03
OK14 OK2026-04-10
ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0.1

READMEYes · 275 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9includes a package overview page
Examples that run: 50%3 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 83%
Help pages citing references: 0%

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #7,800 · ~7/day · ~227/mo

Releases R versions

Daily download trend is not available in this view yet.

37130 days

1.1K90 days

2.7K1 year

Compare downloads with other packages →

Also on70 r2u204 bioconda

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing scROSHI adds 11 packages (9 with compiled code, 19 MB of source tarballs). Heaviest: BH 14 MB, Rcpp 1.8 MB, RcppEigen 1.7 MB. 4 more not on CRAN are not measured.

Depends (1)

R >= 3.6

Imports (7)

limma S4Vectors SingleCellExperimentstatsSummarizedExperimentutilsuwot

LinkingTo (0)

none

Suggests (0)

none

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 (3)

Dominik Burri

Author, Maintainer since 1.0.0.1 (2026) · added in 1.0.0.1

Lars Bosshard

Author

Michael Prummer

Author

Previously maintained by Lars Bosshard (1.0.0.0).

Releases (2)

Pick two releases to compare their code metrics.

1.0.0.1Latest
record
2026-09-09 · current release · diff ↗
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
1.0.0.0
record
2023-01-10
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-01-10
Total releases: 2 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6
Bundled data: 668 KB / 3 files
Download size: 682 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scROSHI")

Format

Burri, D., Bosshard, L., & Prummer, M. (2026). scROSHI: Robust Supervised Hierarchical Identification of Single Cells (Version 1.0.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.scROSHI

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 scROSHI version 1.0.0.1 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, 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 →