{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T14:25:54Z","timestamp":1782311154131,"version":"3.54.5"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,3,30]],"date-time":"2023-03-30T00:00:00Z","timestamp":1680134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFA1106000"],"award-info":[{"award-number":["2022YFA1106000"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32222026"],"award-info":[{"award-number":["32222026"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170660"],"award-info":[{"award-number":["32170660"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32000561"],"award-info":[{"award-number":["32000561"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Rising Star Program","award":["21QA1408200"],"award-info":[{"award-number":["21QA1408200"]}]},{"DOI":"10.13039\/100007219","name":"Natural Science Foundation of Shanghai","doi-asserted-by":"publisher","award":["21ZR1467600"],"award-info":[{"award-number":["21ZR1467600"]}],"id":[{"id":"10.13039\/100007219","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["20002150073"],"award-info":[{"award-number":["20002150073"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Bioinformatics Supercomputer Center of Tongji University for Offering Computing Resources"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Single-cell CRISPR screens have been widely used to investigate gene regulatory circuits in diverse biological systems. The recent development of single-cell CRISPR screens has enabled multimodal profiling of perturbed cells with both gene expression, chromatin accessibility and protein levels. However, current methods cannot meet the analysis requirements of different types of data and have limited functions. Here, we introduce Single-cell CRISPR screens data analysEs and perturbation modEling (SCREE) as a comprehensive and flexible pipeline to facilitate the analyses of various types of single-cell CRISPR screens data. SCREE performs read alignment, sgRNA assignment, quality control, clustering and visualization, perturbation enrichment evaluation, perturbation efficiency modeling, gene regulatory score calculation and functional analyses of perturbations for single-cell CRISPR screens with both RNA, ATAC and multimodal readout. SCREE is available at https:\/\/github.com\/wanglabtongji\/SCREE.<\/jats:p>","DOI":"10.1093\/bib\/bbad123","type":"journal-article","created":{"date-parts":[[2023,3,31]],"date-time":"2023-03-31T14:51:15Z","timestamp":1680274275000},"source":"Crossref","is-referenced-by-count":8,"title":["SCREE: a comprehensive pipeline for single-cell multi-modal CRISPR screen data processing and analysis"],"prefix":"10.1093","volume":"24","author":[{"given":"Hailin","family":"Wei","sequence":"first","affiliation":[{"name":"Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education , Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, , 200092 , China"},{"name":"Tongji University , Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, , 200092 , China"},{"name":"Frontier Science Center for Stem Cells , School of Life Science and Technology, , Shanghai 200092 , China"},{"name":"Tongji University , School of Life Science and Technology, , Shanghai 200092 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tong","family":"Han","sequence":"additional","affiliation":[{"name":"Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education , Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, , 200092 , China"},{"name":"Tongji University , Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, , 200092 , China"},{"name":"Frontier Science Center for Stem Cells , School of Life Science and Technology, , Shanghai 200092 , China"},{"name":"Tongji University , School of Life Science and Technology, , Shanghai 200092 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taiwen","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oral Diseases , National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, , Chengdu 610041 , China"},{"name":"Sichuan University , National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, , Chengdu 610041 , China"},{"name":"Jiangsu Key Lab of Cancer Biomarkers , Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, , Nanjing, 211166 , China"},{"name":"Nanjing Medical University , Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, , Nanjing, 211166 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiu","family":"Wu","sequence":"additional","affiliation":[{"name":"Frontier Science Center for Stem Cells , School of Life Science and Technology, , Shanghai 200092 , China"},{"name":"Tongji University , School of Life Science and Technology, , Shanghai 200092 , China"},{"name":"Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital , School of Life Sciences and Technology, , Shanghai 200092 , China"},{"name":"Tongji University , School of Life Sciences and Technology, , Shanghai 200092 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenfei","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education , Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, , 200092 , China"},{"name":"Tongji University , Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, , 200092 , China"},{"name":"Frontier Science Center for Stem Cells , School of Life Science and Technology, , Shanghai 200092 , China"},{"name":"Tongji University , School of Life Science and Technology, , Shanghai 200092 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,3,30]]},"reference":[{"issue":"6166","key":"2023052022112613700_ref1","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1126\/science.1246981","article-title":"Genetic screens in human cells using the CRISPR-Cas9 system","volume":"343","author":"Wang","year":"2014","journal-title":"Science"},{"issue":"6166","key":"2023052022112613700_ref2","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1126\/science.1247005","article-title":"Genome-scale CRISPR-Cas9 knockout screening in human cells","volume":"343","author":"Shalem","year":"2014","journal-title":"Science"},{"issue":"7501","key":"2023052022112613700_ref3","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/nature13166","article-title":"High-throughput screening of a CRISPR\/Cas9 library for functional genomics in human 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