A benchmark of algorithms for the analysis of pooled CRISPR screens.
Benchmarking
CRISPR activation
CRISPR interference
CRISPR knockoout
CRISPR screen
Screen algorithms
Simulation
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
09 03 2020
09 03 2020
Historique:
entrez:
11
3
2020
pubmed:
11
3
2020
medline:
20
2
2021
Statut:
epublish
Résumé
Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, we provide a review of the commonly used algorithms in the computational analysis of pooled CRISPR screens. We develop a comprehensive simulation framework to benchmark and compare the performance of these algorithms using both synthetic and real datasets. Our findings inform parameter choices of CRISPR screens and provide guidance to researchers on the design and analysis of pooled CRISPR screens.
Identifiants
pubmed: 32151271
doi: 10.1186/s13059-020-01972-x
pii: 10.1186/s13059-020-01972-x
pmc: PMC7063732
doi:
Substances chimiques
RNA, Small Interfering
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
62Subventions
Organisme : NIMHD NIH HHS
ID : R21 MD012867
Pays : United States
Organisme : NIA NIH HHS
ID : P30 AG059307
Pays : United States
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