R Observatory: Metrics for DIscBIO version 1.2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DIscBIO

1.2.3Package record

A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics

0packages depend

4.8Kdownloads / year

–test coverage

9/13flavors OK

Overview

About

Maintained by Waldir LeoncioCRAN page ↗GitHub ↗Issues ↗

An open, multi-algorithmic pipeline for easy, fast and efficient analysis of cellular sub-populations and the molecular signatures that characterize them. The pipeline consists of four successive steps: data pre-processing, cellular clustering with pseudo-temporal ordering, defining differential expressed genes and biomarker identification. More details on Ghannoum et. al. (2021) doi:10.3390/ijms22031399. This package implements extensions of the work published by Ghannoum et. al. (2019) doi:10.1101/700989.

Changes in 1.2.3

Delinted package
Removed dependency on philentropy and org.Hs.eg.db (issue #44, #45)

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("DIscBIO", 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("ocbe-uio/DIscBIO")

Development version from ocbe-uio/DIscBIO. 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-discbio

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

2ERROR2NOTE9OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package required but not available: ‘TSCAN’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘DISCBIO.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 9.2 min · r-oldrel-windows-x86_64

Status changes

ERROR9 OK, 2 NOTE, 2 ERRORNow
ERROR9 OK, 5 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.3

README· In the repository, left out of the releaseVignettesNoNEWSYes · 100% structured · mentions 1.2.3Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 51
Examples that run: 89%8 run in a plain check · 1 hold no code
Exported functions with examples: 19%
Documented parameters: 100%
Return-value docs: 94%
Help pages citing references: 2%

How these are measured

Downloads

4.8K

CRAN downloads in the past year

Rank #8,751 · ~13/day · ~402/mo

Releases R versions

Daily download trend is not available in this view yet.

35930 days

1.1K90 days

4.8K1 year

Compare downloads with other packages →

Also on114 r2u37 c2d4u

How downloads are counted

Repository

ocbe-uio/discbio ↗Organization: ocbe-uio

14Stars

5Forks

3Open issues

0Open PRs

6Releases

862Commits

5Commit identities

transcriptomicsbiomarker-discoverysingle-cell-analysisscrna-seqjupyter-notebookr-package

862 commits · Last activity 2026-01-09 · 0% stars, 30d · Default branch at 1.2.3.9001, ahead of CRAN 1.2.3 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 94%
Median days to close, 50 most recently updated closed issues: 7
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-05 · 132026-07-07 · 14

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/ocbe-uio/discbio on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (3)

Contributing guideIssue templatesPR template

Coverage (1)

Coverage reporting

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (1)

Lint workflow

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing DIscBIO adds 46 packages (23 with compiled code, 42 MB of source tarballs). Heaviest: RWekajars 9.6 MB, ggplot2 6.0 MB, igraph 4.8 MB. 3 more not on CRAN are not measured.

Depends (2)

R >= 4.0SingleCellExperiment

Imports (23)

methodsTSCAN httr mclust statmod igraph RWeka vegan NetIndices pnggrDevicesRColorBrewer ggplot2rpartfpcclusterrpart.plot tsnegraphicsstatsutilsimpute withr

LinkingTo (0)

none

Suggests (4)

testthat Seurat org.Hs.eg.db AnnotationDbi

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 (4)

Waldir Leoncio

Maintainer since 1.0.0 (2020), Author

Salim Ghannoum

Author, Copyright holder

Alvaro Köhn-Luque

Author, Thesis advisor

Damiano Fantini

Contributor

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.2.3Latest
record
2026-01-08 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2.2
record
2023-11-06 · diff ↗
1.2.1
record
2023-10-09 · diff ↗
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
1.2.0
record
2021-04-28 · diff ↗
1.1.0
record
2020-11-13 · diff ↗
1.0.1
record
2020-10-06 · diff ↗
1.0.0
record
2020-08-26
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-08-26
Total releases: 7 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0
Bundled data: 1.6 MB / 3 files
Download size: 1.1 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DIscBIO")

Format

Leoncio, W., Fantini, D., Ghannoum, S., & Köhn-Luque, A. (2026). DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics (Version 1.2.3) [Computer software]. https://doi.org/10.32614/CRAN.package.DIscBIO

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 DIscBIO version 1.2.3 [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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