{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T16:07:54Z","timestamp":1780589274923,"version":"3.54.1"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,7,6]],"date-time":"2020-07-06T00:00:00Z","timestamp":1593993600000},"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\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61721003"],"award-info":[{"award-number":["61721003"]}],"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":["81890993"],"award-info":[{"award-number":["81890993"]}],"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":["61922047"],"award-info":[{"award-number":["61922047"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Molecular heterogeneities and complex microenvironments bring great challenges for cancer diagnosis and treatment. Recent advances in single-cell RNA-sequencing (scRNA-seq) technology make it possible to study cancer cell heterogeneities and microenvironments at single-cell transcriptomic level. Here, we develop an R package named scCancer, which focuses on processing and analyzing scRNA-seq data for cancer research. Except basic data processing steps, this package takes several special considerations for cancer-specific features. Firstly, the package introduced comprehensive quality control metrics. Secondly, it used a data-driven machine learning algorithm to accurately identify major cancer microenvironment cell populations. Thirdly, it estimated a malignancy score to classify malignant (cancerous) and non-malignant cells. Then, it analyzed intra-tumor heterogeneities by key cellular phenotypes (such as cell cycle and stemness), gene signatures and cell\u2013cell interactions. Besides, it provided multi-sample data integration analysis with different batch-effect correction strategies. Finally, user-friendly graphic reports were generated for all the analyses. By testing on 56 samples with 433\u00a0405 cells in total, we demonstrated its good performance. The package is available at: http:\/\/lifeome.net\/software\/sccancer\/.<\/jats:p>","DOI":"10.1093\/bib\/bbaa127","type":"journal-article","created":{"date-parts":[[2020,5,25]],"date-time":"2020-05-25T15:13:20Z","timestamp":1590419600000},"source":"Crossref","is-referenced-by-count":62,"title":["scCancer: a package for automated processing of single-cell RNA-seq data in cancer"],"prefix":"10.1093","volume":"22","author":[{"given":"Wenbo","family":"Guo","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongfang","family":"Wang","sequence":"additional","affiliation":[{"name":"BIOPIC and School of Life Sciences, Peking University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shicheng","family":"Wang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiran","family":"Shan","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changyi","family":"Liu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin","family":"Gu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua 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