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

Featured publications

• Barry et al., 2024+. “Robust differential expression testing…”. Genome Biology.
• Barry et al., 2024. “Exponential family measurement error models…”. Biostatistics.
• Morris et al., 2023. “Discovery of target genes and pathways…”. Science.
• Barry et al., 2021. “SCEPTRE improves calibration and sensitivity…”. Genome Biology.

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 feature requests, please start a discussion under feature requests. For questions about sceptre functionality, documentation, or how to apply it to your data, please start a discussion under Q&A.