A benchmark of algorithms for the analysis of pooled CRISPR screens
Abstract 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...
Ausführliche Beschreibung
Autor*in: |
Bodapati, Sunil [verfasserIn] Daley, Timothy P. [verfasserIn] Lin, Xueqiu [verfasserIn] Zou, James [verfasserIn] Qi, Lei S. [verfasserIn] |
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E-Artikel |
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Sprache: |
Englisch |
Erschienen: |
2020 |
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Übergeordnetes Werk: |
Enthalten in: Genome biology - London : BioMed Central, 2000, 21(2020), 1 vom: 09. März |
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Übergeordnetes Werk: |
volume:21 ; year:2020 ; number:1 ; day:09 ; month:03 |
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DOI / URN: |
10.1186/s13059-020-01972-x |
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Katalog-ID: |
SPR03903769X |
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10.1186/s13059-020-01972-x doi (DE-627)SPR03903769X (SPR)s13059-020-01972-x-e DE-627 ger DE-627 rakwb eng 570 ASE 42.13 bkl 42.20 bkl Bodapati, Sunil verfasserin aut A benchmark of algorithms for the analysis of pooled CRISPR screens 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract 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. CRISPR screen (dpeaa)DE-He213 CRISPR knockoout (dpeaa)DE-He213 CRISPR interference (dpeaa)DE-He213 CRISPR activation (dpeaa)DE-He213 Benchmarking (dpeaa)DE-He213 Screen algorithms (dpeaa)DE-He213 Simulation (dpeaa)DE-He213 Daley, Timothy P. verfasserin aut Lin, Xueqiu verfasserin aut Zou, James verfasserin aut Qi, Lei S. verfasserin aut Enthalten in Genome biology London : BioMed Central, 2000 21(2020), 1 vom: 09. März (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:21 year:2020 number:1 day:09 month:03 https://dx.doi.org/10.1186/s13059-020-01972-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 42.13 ASE 42.20 ASE AR 21 2020 1 09 03 |
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10.1186/s13059-020-01972-x doi (DE-627)SPR03903769X (SPR)s13059-020-01972-x-e DE-627 ger DE-627 rakwb eng 570 ASE 42.13 bkl 42.20 bkl Bodapati, Sunil verfasserin aut A benchmark of algorithms for the analysis of pooled CRISPR screens 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract 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. CRISPR screen (dpeaa)DE-He213 CRISPR knockoout (dpeaa)DE-He213 CRISPR interference (dpeaa)DE-He213 CRISPR activation (dpeaa)DE-He213 Benchmarking (dpeaa)DE-He213 Screen algorithms (dpeaa)DE-He213 Simulation (dpeaa)DE-He213 Daley, Timothy P. verfasserin aut Lin, Xueqiu verfasserin aut Zou, James verfasserin aut Qi, Lei S. verfasserin aut Enthalten in Genome biology London : BioMed Central, 2000 21(2020), 1 vom: 09. März (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:21 year:2020 number:1 day:09 month:03 https://dx.doi.org/10.1186/s13059-020-01972-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 42.13 ASE 42.20 ASE AR 21 2020 1 09 03 |
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10.1186/s13059-020-01972-x doi (DE-627)SPR03903769X (SPR)s13059-020-01972-x-e DE-627 ger DE-627 rakwb eng 570 ASE 42.13 bkl 42.20 bkl Bodapati, Sunil verfasserin aut A benchmark of algorithms for the analysis of pooled CRISPR screens 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract 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. CRISPR screen (dpeaa)DE-He213 CRISPR knockoout (dpeaa)DE-He213 CRISPR interference (dpeaa)DE-He213 CRISPR activation (dpeaa)DE-He213 Benchmarking (dpeaa)DE-He213 Screen algorithms (dpeaa)DE-He213 Simulation (dpeaa)DE-He213 Daley, Timothy P. verfasserin aut Lin, Xueqiu verfasserin aut Zou, James verfasserin aut Qi, Lei S. verfasserin aut Enthalten in Genome biology London : BioMed Central, 2000 21(2020), 1 vom: 09. März (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:21 year:2020 number:1 day:09 month:03 https://dx.doi.org/10.1186/s13059-020-01972-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 42.13 ASE 42.20 ASE AR 21 2020 1 09 03 |
allfieldsGer |
10.1186/s13059-020-01972-x doi (DE-627)SPR03903769X (SPR)s13059-020-01972-x-e DE-627 ger DE-627 rakwb eng 570 ASE 42.13 bkl 42.20 bkl Bodapati, Sunil verfasserin aut A benchmark of algorithms for the analysis of pooled CRISPR screens 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract 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. CRISPR screen (dpeaa)DE-He213 CRISPR knockoout (dpeaa)DE-He213 CRISPR interference (dpeaa)DE-He213 CRISPR activation (dpeaa)DE-He213 Benchmarking (dpeaa)DE-He213 Screen algorithms (dpeaa)DE-He213 Simulation (dpeaa)DE-He213 Daley, Timothy P. verfasserin aut Lin, Xueqiu verfasserin aut Zou, James verfasserin aut Qi, Lei S. verfasserin aut Enthalten in Genome biology London : BioMed Central, 2000 21(2020), 1 vom: 09. März (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:21 year:2020 number:1 day:09 month:03 https://dx.doi.org/10.1186/s13059-020-01972-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 42.13 ASE 42.20 ASE AR 21 2020 1 09 03 |
allfieldsSound |
10.1186/s13059-020-01972-x doi (DE-627)SPR03903769X (SPR)s13059-020-01972-x-e DE-627 ger DE-627 rakwb eng 570 ASE 42.13 bkl 42.20 bkl Bodapati, Sunil verfasserin aut A benchmark of algorithms for the analysis of pooled CRISPR screens 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract 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. CRISPR screen (dpeaa)DE-He213 CRISPR knockoout (dpeaa)DE-He213 CRISPR interference (dpeaa)DE-He213 CRISPR activation (dpeaa)DE-He213 Benchmarking (dpeaa)DE-He213 Screen algorithms (dpeaa)DE-He213 Simulation (dpeaa)DE-He213 Daley, Timothy P. verfasserin aut Lin, Xueqiu verfasserin aut Zou, James verfasserin aut Qi, Lei S. verfasserin aut Enthalten in Genome biology London : BioMed Central, 2000 21(2020), 1 vom: 09. März (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:21 year:2020 number:1 day:09 month:03 https://dx.doi.org/10.1186/s13059-020-01972-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 42.13 ASE 42.20 ASE AR 21 2020 1 09 03 |
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570 ASE 42.13 bkl 42.20 bkl A benchmark of algorithms for the analysis of pooled CRISPR screens CRISPR screen (dpeaa)DE-He213 CRISPR knockoout (dpeaa)DE-He213 CRISPR interference (dpeaa)DE-He213 CRISPR activation (dpeaa)DE-He213 Benchmarking (dpeaa)DE-He213 Screen algorithms (dpeaa)DE-He213 Simulation (dpeaa)DE-He213 |
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A benchmark of algorithms for the analysis of pooled CRISPR screens |
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Abstract 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. |
abstractGer |
Abstract 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. |
abstract_unstemmed |
Abstract 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. |
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score |
7.398056 |