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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 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 ondisc 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.

ondisc is a companion package to sceptre, an R package for statistically rigorous and user-friendly single-cell CRISPR screen analysis. Although ondisc and sceptre work best in conjunction, ondisc can be used independently of sceptre (and conversely, sceptre can be used independently of ondisc). Users can submit issues on the ondisc Github page.