ondisc
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.