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sceptre

sceptre is an R package for single-cell CRISPR screen data analysis, emphasizing statistical rigor, massive scalability, and ease of use.

v0.10.0: sceptre at massive scale

sceptre v0.10.0 represents another a major upgrade to the sceptre software. We have integrated sceptre with ondisc, a companion R package that facilitates large-scale computing on single-cell data. sceptre now supports the analysis of single-cell CRISPR screen data out-of-core on a laptop or distributed across hundreds of processors on a computing cluster or cloud.

sceptre v0.10.0 includes the following updates:

  • Support for disk-backed sceptre objects, enabling the analysis of data too large to fit in memory
  • A sceptre Nextflow pipeline, enabling the deployment of sceptre across hundreds of processors on a cluster or cloud
  • An updated e-book containing new sections about at-scale sceptre and the statistical methodology underlying sceptre
  • New functionality for plotting and inspecting gRNA-to-cell assignments
  • A comprehensive suite of unit tests, which verify the correctness of the code
  • More detailed man pages (including runnable examples) and minor bug fixes

You can see our RECOMB poster for more information about this update.

sceptre also recently was featured in a 10x Genomics analysis guide.

Bug reports, feature requests, and software questions

For bug reports, please open a GitHub issue. For questions about sceptre functionality, documentation, or how to apply it to your data, please start a discussion under Q&A.