R Observatory: Metrics for ondisc version 1.3.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ondisc

1.3.5Package record

Algorithms and Data Structures for Large Single-Cell Expression Matrices

0packages depend

1.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Timothy BarryCRAN page ↗GitHub ↗Website ↗Issues ↗

Single-cell datasets are growing in size, posing challenges as well as opportunities for genomics researchers. 'ondisc' is an R package that facilitates analysis of large-scale single-cell data out-of-core on a laptop or distributed across tens to hundreds of processors on a cluster or cloud. In both of these settings, 'ondisc' requires only a few gigabytes of memory, even if the input data are tens of gigabytes in size. 'ondisc' mainly is oriented toward single-cell CRISPR screen analysis, but also can be used for single-cell differential expression and single-cell co-expression analyses. 'ondisc' is powered by several new, efficient algorithms for manipulating and querying large, sparse expression matrices.

Install

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

install.packages("ondisc", 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("timothy-barry/ondisc")

Development version from timothy-barry/ondisc. 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-ondisc

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: 22.4 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-09-25
ERROR12 OK, 1 ERROR2026-09-18
OK13 OK2026-08-26
ERROR12 OK, 1 ERROR2026-08-22
OK13 OK2026-08-20

Show 16 earlier changesHide 16 earlier changes

ERROR12 OK, 1 ERROR2026-08-12
OK13 OK2026-08-08
ERROR12 OK, 1 ERROR2026-08-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-03
ERROR12 OK, 1 ERROR2026-08-02
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-30
NOTE12 OK, 1 NOTE2026-07-29
OK13 OK2026-07-26
ERROR12 OK, 1 ERROR2026-07-19
OK13 OK2026-07-08
ERROR12 OK, 1 ERROR2026-07-05
OK13 OK2026-06-25
ERROR11 OK, 1 ERROR2026-06-24
OK7 OK2026-06-18

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.5

READMEYes · 165 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · does not mention 1.3.5Citation fileNoWebsiteYes · pkgdown

Help pages: 8includes a package overview page
Examples that run: 100%8 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Getting started with ondisc HTML

How these are measured

Downloads

1.8K

CRAN downloads in the past year

Rank #7,391 · ~5/day · ~152/mo

Releases R versions

Daily download trend is not available in this view yet.

42230 days

1.2K90 days

1.8K1 year

Compare downloads with other packages →

Also on387 r2u

How downloads are counted

Repository

timothy-barry/ondisc ↗Account: timothy-barry

12Stars

6Forks

1Open issues

1Open PRs

2Releases

338Commits

10Commit identities

338 commits · Last activity 2026-07-31 · +9.1% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 83%
Median days to close, 50 most recently updated closed issues: 16
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-03-20 · 102026-10-15 · 12

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/timothy-barry/ondisc on 2026-10-21.

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-07-31

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

AI coding toolsBeta

An outside contributor's pull request to this repository was written with an AI coding tool.

From outside contributors

Claude Code
Pull requests: 1 from outside contributors, first on 2025-06-20, 1 from forks

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing ondisc adds 28 packages (16 with compiled code, 15 MB of source tarballs). Heaviest: data.table 5.7 MB, Rcpp 1.8 MB, vctrs 1.0 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 4.1.0

Imports (8)

crayon data.tablemethodsRcpp Rhdf5lib dplyr readrMatrix

LinkingTo (2)

Rcpp Rhdf5lib

Suggests (5)

sessioninfo knitr R.utils rmarkdown testthat

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)

Timothy Barry

Author, Maintainer since 1.0.0 (2021)

Eugene Katsevich

Author, Thesis advisor

Songcheng Dai

Contributor · added in 1.3.5

Yixuan Qiu

Contributor · added in 1.3.5

Listed in earlier versions (1)

Kathryn Roeder

no longer listed · 1.0.0

Releases (2)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-06-17
1.3.5Latest
record
2026-06-17 · current release · diff ↗ ·
removed 9 exports
create_ondisc_matrix_from_mtx, get_cell_barcodes, get_feature_ids, get_feature_names, metadata_ondisc_matrix, multimodal_ondisc_matrix, ncol, nrow, ondisc_matrix

added 4 exports
create_odm_from_cellranger, create_odm_from_r_matrix, initialize_odm_from_backing_file, write_example_cellranger_dataset
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2025-02-02
issues were not corrected in time
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
1.0.0
record
2021-03-05
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-03-05
Total releases: 2 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 251 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ondisc")

Format

Barry, T., Dai, S., Katsevich, E., & Qiu, Y. (2026). ondisc: Algorithms and Data Structures for Large Single-Cell Expression Matrices (Version 1.3.5) [Computer software]. https://doi.org/10.32614/CRAN.package.ondisc

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 ondisc version 1.3.5 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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