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ondisc: Algorithms and Data Structures for Large Single-Cell Expression
Matrices
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.
| Version: |
1.3.5 |
| Depends: |
R (≥ 4.1.0) |
| Imports: |
crayon, data.table, methods, Rcpp, Rhdf5lib, dplyr, readr, Matrix |
| LinkingTo: |
Rcpp, Rhdf5lib |
| Suggests: |
sessioninfo, knitr, R.utils, rmarkdown, testthat (≥ 3.0.0) |
| Published: |
2026-06-17 |
| DOI: |
10.32614/CRAN.package.ondisc |
| Author: |
Timothy Barry 
[aut, cre],
Songcheng Dai [ctb],
Yixuan Qiu [ctb],
Eugene Katsevich [aut, ths] |
| Maintainer: |
Timothy Barry <tbarry at hsph.harvard.edu> |
| BugReports: |
https://github.com/timothy-barry/ondisc/issues |
| License: |
MIT + file LICENSE |
| URL: |
https://timothy-barry.github.io/ondisc/,
https://timothy-barry.github.io/sceptre-book/ |
| NeedsCompilation: |
yes |
| SystemRequirements: |
GNU make |
| Materials: |
README, NEWS |
| CRAN checks: |
ondisc results |
Documentation:
Downloads:
Linking:
Please use the canonical form
https://CRAN.R-project.org/package=ondisc
to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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