DESCRIPTION

Package: sceptre
Title: Analysis of Single-Cell CRISPR Screen Data
Version: 0.10.2
Authors@R: 
    c(person(given = "Timothy",
           family = "Barry",
           role = c("aut", "cre"),
           email = "tbarry@hsph.harvard.edu",
           comment=c(ORCID="0000-0002-4356-627X")),
           person(given = "Joseph",
           family = "Deutsch",
           role = c("aut")),
           person(given = "Eugene",
           family = "Katsevich",
           role = c("aut"),
           email = "ekatsevi@wharton.upenn.edu")
           )
Description: `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.
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
LinkingTo: Rcpp, BH
biocViews: CRISPR, SingleCell, DifferentialExpression, GeneRegulation, DataImport, GeneTarget
Imports:
    BH,
    cowplot,
    crayon,
    data.table,
    dplyr,
    ggplot2,
    Matrix,
    methods,
    Rcpp (>= 1.0.9),
    scales,
    stats,
    purrr
Depends: 
    R (>= 4.1)
Suggests:
    ondisc,
    R.utils,
    sessioninfo,
    rmarkdown,
    knitr,
    parallel,
    testthat (>= 3.0.0),
    magrittr,
    MASS
Remotes: github::timothy-barry/ondisc
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://timothy-barry.github.io/sceptre-book/, https://github.com/Katsevich-Lab/sceptre
LazyDataCompression: gzip
LazyData: true