R Observatory: Metrics for rPanglaoDB version 0.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rPanglaoDB

0.2.1Package record

Download and Merge Single-Cell RNA-Seq Data from the PanglaoDB Database

0packages depend

2.9Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Daniel OsorioCRAN page ↗GitHub ↗

Download and merge labeled single-cell RNA-seq data from the PanglaoDB https://panglaodb.se/ into a Seurat object.

Install

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

install.packages("rPanglaoDB", 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("dosorio/rPanglaoDB")

Development version from dosorio/rPanglaoDB. 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-rpanglaodb

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-rPanglaoDB

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-rPanglaoDB

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

1ERROR12OK

Check messages

ERRORexamplesr-oldrel-macos-arm64

Running examples in ‘rPanglaoDB-Ex.R’ failed
The error most likely occurred in:

> ### Name: getSampleComposition
> ### Title: Get the cell-type content for each sample from the panglaoDB
> ###   database.
> ### Aliases: getSampleComposition
> 
> ### ** Examples
> 
> # From PanglaoDB
> # https://panglaodb.se/list_clusters_and_cell_types.html?sra=SRA689041&srs=SRS3166675
> 
> SRS3166675 <- getSampleComposition(srs = 'SRS3166675')
Error in curl::curl_download(url, file, quiet = quiet, mode = mode, handle = handle) : 
  Timeout was reached [panglaodb.se]: Resolving timed out after 10002 milliseconds
Calls: getSampleComposition ... getSampleList -> <Anonymous> -> <Anonymous> -> raise_libcurl_error
Execution halted

CRAN check page ↗

Slowest check: 7.5 min · r-oldrel-macos-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR13 OK, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.1

READMEYes · 704 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 4
Examples that run: 50%2 run in a plain check · 2 never run
Exported functions with examples: 100%
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 #14,856 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

31830 days

79790 days

2.9K1 year

Compare downloads with other packages →

Also on149 r2u3 autocran47 c2d4u

How downloads are counted

Repository

dosorio/rpanglaodb ↗Account: dosorio

27Stars

1Forks

3Open issues

0Open PRs

0Releases

140Commits

3Commit identities

data-miningdata-integrationsingle-cellrna-seqsingle-cell-rna-seq

140 commits · Last activity 2023-06-01 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2025-05-28 · 262026-07-07 · 27

How these are measured

PracticesBeta

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

Checks run against github.com/dosorio/rpanglaodb on 2026-10-11.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing rPanglaoDB adds 137 packages (83 with compiled code, 128 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (0)

none

Imports (6)

methodsXML xml2 Seurat pbapplyMatrix

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

People & History

People (3)

Daniel Osorio

Author, Maintainer since 0.1.0 (2021)

James J. Cai

Author

Marieke Kuijjer

Author

Releases (3)

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
0.2.1Latest
record
2021-05-13 · current release · diff ↗
0.2.0
record
2021-04-23 · diff ↗
0.1.0
record
2021-04-15
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-04-15
Total releases: 3 / 5 yrs
License: GPL-3 OSI
Download size: 9.8 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("rPanglaoDB")

Format

Osorio, D., Cai, J. J., & Kuijjer, M. (2021). rPanglaoDB: Download and Merge Single-Cell RNA-Seq Data from the PanglaoDB Database (Version 0.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.rPanglaoDB

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 rPanglaoDB version 0.2.1 [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 →