timothy-barry/sceptre: Analysis of Single-Cell CRISPR Screen Data

`sceptre` is an R package for statistically rigorous, massively scalable, and user-friendly single-cell CRISPR screen data analysis. The `sceptre` pipeline consists of several distinct steps: (1) import data from 10X CellRanger, Parse CRISPR Detect, or a set of R objects; (2) set the analysis parameters, which are the parameters that govern how the statistical analysis is to be conducted; (3) assign gRNAs to cells using one of three principled methods; (4) run quality control; (5) run the calibration check, which is an analysis that verifies that `sceptre` controls the rate of false positives on the dataset under analysis; (6) run the power check, which is an analysis that verifies that `sceptre` is capable of discovering true associations on the dataset under analysis; (7) run the discovery analysis to identify high-confidence perturbation-gene links among the set of perturbations and genes whose association status we do not know but seek to learn; (8) write outputs to a specified directory, including results, plots, and a textual summary of the analysis. `sceptre` leverages several novel statistical and computational algorithms to achieve high statistical accuracy and computational speed.

install.packages("remotes")
remotes::install_github("timothy-barry/sceptre")