# ------------------------------------------------
# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "sceptre" in publications use:'
type: software
license: GPL-3.0-only
title: 'sceptre: Analysis of Single-Cell CRISPR Screen Data'
version: 0.99.0
doi: 10.1186/s13059-021-02545-2
identifiers:
- type: doi
  value: 10.32614/CRAN.package.sceptre
- type: url
  value: https://timothy-barry.github.io/sceptre-book/
abstract: '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 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.'
authors:
- family-names: Barry
  given-names: Timothy
  email: tbarry@hsph.harvard.edu
  orcid: https://orcid.org/0000-0002-4356-627X
- family-names: Deutsch
  given-names: Louis
- family-names: Katsevich
  given-names: Eugene
  email: ekatsevi@wharton.upenn.edu
  orcid: https://orcid.org/0000-0003-0598-2050
preferred-citation:
  type: article
  title: SCEPTRE improves calibration and sensitivity in single-cell CRISPR screen
    analysis
  authors:
  - family-names: Barry
    given-names: Timothy
    email: tbarry@hsph.harvard.edu
    orcid: https://orcid.org/0000-0002-4356-627X
  - family-names: Wang
    given-names: Xuran
  - family-names: Morris
    given-names: John A.
  - family-names: Roeder
    given-names: Kathryn
  - family-names: Katsevich
    given-names: Eugene
    email: ekatsevi@wharton.upenn.edu
    orcid: https://orcid.org/0000-0003-0598-2050
  journal: Genome Biology
  year: '2021'
  volume: '22'
  issue: '1'
  publisher:
    name: Springer Nature
  doi: 10.1186/s13059-021-02545-2
  url: https://link.springer.com/article/10.1186/s13059-021-02545-2
  start: '1'
  end: '19'
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/Katsevich-Lab/sceptre
commit: 21f9ea098b69c444a884a49bc254de711968e3b5
url: https://katsevich-lab.github.io/sceptre/
date-released: '2026-08-31'
contact:
- family-names: Barry
  given-names: Timothy
  email: tbarry@hsph.harvard.edu
  orcid: https://orcid.org/0000-0002-4356-627X
references:
- type: article
  title: Exponential family measurement error models for single-cell CRISPR screens
  authors:
  - family-names: Barry
    given-names: Timothy
  - family-names: Roeder
    given-names: Kathryn
  - family-names: Katsevich
    given-names: Eugene
  journal: Biostatistics
  year: '2024'
  publisher:
    name: Oxford University Press
  doi: 10.1093/biostatistics/kxae010
  url: https://doi.org/10.1093/biostatistics/kxae010
  start: kxae010
- type: article
  title: Robust differential expression testing for single-cell CRISPR screens at
    low multiplicity of infection
  authors:
  - family-names: Barry
    given-names: Timothy
  - family-names: Mason
    given-names: Kaishu
  - family-names: Roeder
    given-names: Kathryn
  - family-names: Katsevich
    given-names: Eugene
  journal: Genome Biology
  year: '2024'
  volume: '25'
  issue: '124'
  publisher:
    name: Springer Nature
  doi: 10.1186/s13059-024-03254-2
  url: https://link.springer.com/article/10.1186/s13059-024-03254-2
  start: '1'
  end: '30'