sceptre

An R package for single-cell CRISPR screen data analysis, emphasizing statistical rigor, computational efficiency, and ease of use.

Release of sceptre v0.9.2

We are excited to announce the release of sceptre v0.9.2, a substantial update to the package. This milestone includes the following developments:

• A reimagined user experience based on a modular, object-oriented workflow.
• Further improvements in speed and memory efficiency.
• A unified interface for low- and high-MOI analyses.
• A suite of plotting functions facilitating visualization of each step in the pipeline.
• Expanded support for gRNA assignment and quality control.
• Interoperability with output from 10X Cell Ranger and Parse Biosciences CRISPR Detect.
• An e-book guiding users through the entire process of analyzing their data using sceptre.

sceptre v0.9.2 facilitates an entire analysis pipeline for single-cell CRISPR screens, starting from UMI count data obtained from tools like 10X Cell Ranger.

Featured publications

• Morris et al., 2023. “Discovery of target genes and pathways…”. Science.
• Barry et al., 2021. “SCEPTRE improves calibration and sensitivity…”. Genome Biology.

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.