R Observatory: Metrics for DamageDetective version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DamageDetective

1.0.0Package record

Detecting Damaged Cells in Single-Cell RNA Sequencing Data

0packages depend

2.2Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Alicen HenningCRAN page ↗GitHub ↗Website ↗Issues ↗

Detects and filters damaged cells in single-cell RNA sequencing (scRNA-seq) data using a novel approach inspired by 'DoubletFinder'. Damage is detected by measuring the extent to which cells deviate from artificially damaged profiles of themselves, simulated through the probabilistic escape of cytoplasmic RNA. As output, a damage score ranging from 0 to 1 is given for each cell providing an intuitive scale for filtering that is standardised across cell types, samples, and experiments.

Changes in 1.0.0

CRAN submission comments have been received and addressed.
Fixed DOI formatting.
Fixed spacing in the vignette.
Ensured code lines are shorter than 80 characters for good practice.

From NEWS.md in the release

Install

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

install.packages("DamageDetective", 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("alicenjoyhenning/DamageDetective")

Development version from alicenjoyhenning/DamageDetective. 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-damagedetective

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-DamageDetective

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-DamageDetective

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: 8.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-10

Show 2 earlier changesHide 2 earlier changes

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

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 67% structured · mentions 1.0.0Citation fileNoWebsiteYes · pkgdown

Help pages: 10 (6 internal)
Examples that run: 100%3 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 10%

Vignettes (1)

Damage cell quality control HTML

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #17,170 · ~6/day · ~187/mo

Releases R versions

Daily download trend is not available in this view yet.

24730 days

74690 days

2.2K1 year

Compare downloads with other packages →

Also on74 r2u10 autocran

How downloads are counted

Repository

alicenjoyhenning/damagedetective ↗Account: AlicenJoyHenning

3Stars

0Forks

1Open issues

0Open PRs

1Releases

167Commits

1Commit identities

License file reads as AGPL-3.0 · 167 commits · Last activity 2026-10-13 · 0% stars, 30d · Default branch at 2.0.15, ahead of CRAN 1.0.0 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 67%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-29 · 22026-07-07 · 3

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/alicenjoyhenning/damagedetective on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-13 · The repository has a site deploy workflow

pkgdown site last built 2026-10-13

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing DamageDetective adds 70 packages (34 with compiled code, 67 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, doBy 4.3 MB.

Depends (1)

R >= 4.4.0

Imports (11)

cowplot dplyr ggplot2 ggpubrMatrixpatchwork scales RcppHNSW rlang tidyr withr

LinkingTo (0)

none

Suggests (4)

Seurat knitr rmarkdown spelling

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 (1)

Alicen Henning

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.0Latest
record
2025-04-03 · current release
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-04-03
Total releases: 1 / 1 yrs
License: AGPL (>= 3) OSI
Minimum R: ≥ 4.4.0
Bundled data: 506 KB / 1 file
Download size: 814 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DamageDetective")

Format

Henning, A. (2025). DamageDetective: Detecting Damaged Cells in Single-Cell RNA Sequencing Data (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.DamageDetective

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 DamageDetective version 1.0.0 [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.

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