ondisc
Algorithms and Data Structures for Large Single-Cell Expression Matrices
Description
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.
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CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 25, 2026
ERROR 11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 24, 2026
tests
Running 'testthat.R' [116s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(ondisc)
>
> test_check("ondisc")
[1] "seed: 183623"
[1] "Generating example dataset 1."
[1] "Testing import from
...[truncated]...
1. ├─Matrix::colSums(...) at test-import_from_cellranger_v2.R:130:11
2. └─Matrix::colSums(...)
3. └─base::colSums(x, na.rm = na.rm, dims = dims, ...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 158 ]
Error:
! Test failures.
Execution halted