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For: Freytag S, Tian L, Lönnstedt I, Ng M, Bahlo M. Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data. F1000Res 2018;7:1297. [PMID: 30228881 PMCID: PMC6124389 DOI: 10.12688/f1000research.15809.2] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/14/2018] [Indexed: 12/23/2022]  Open
Number Cited by Other Article(s)
1
Yu J, Yu J, Kang Z, Peng Y. Integration of single-cell sequencing and mendelian randomization reveals novel causal pathways between monocytes and hepatocellular carcinoma. Discov Oncol 2025;16:604. [PMID: 40272662 PMCID: PMC12021761 DOI: 10.1007/s12672-025-02357-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Accepted: 04/09/2025] [Indexed: 04/27/2025]  Open
2
Zhao B, Song K, Wei DQ, Xiong Y, Ding J. scCobra allows contrastive cell embedding learning with domain adaptation for single cell data integration and harmonization. Commun Biol 2025;8:233. [PMID: 39948393 PMCID: PMC11825689 DOI: 10.1038/s42003-025-07692-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 02/06/2025] [Indexed: 02/16/2025]  Open
3
Bramon Mora B, Lindsay H, Thiébaut A, Stuart KD, Gottardo R. tagtango: an application to compare single-cell annotations. Bioinformatics 2025;41:btaf012. [PMID: 39798134 PMCID: PMC11814489 DOI: 10.1093/bioinformatics/btaf012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 12/11/2024] [Accepted: 01/08/2025] [Indexed: 01/15/2025]  Open
4
Yang T, Zhang N, Yang N. Single-cell sequencing in diabetic retinopathy: progress and prospects. J Transl Med 2025;23:49. [PMID: 39806376 PMCID: PMC11727737 DOI: 10.1186/s12967-024-06066-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Accepted: 12/30/2024] [Indexed: 01/16/2025]  Open
5
Nasrollahi FSF, Silva FN, Liu S, Chaudhuri S, Yu M, Wang J, Nho K, Saykin AJ, Bennett DA, Sporns O, Fortunato S. Cell Type Differentiation Using Network Clustering Algorithms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.04.626793. [PMID: 39677670 PMCID: PMC11643020 DOI: 10.1101/2024.12.04.626793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
6
Goggin SM, Zunder ER. ESCHR: a hyperparameter-randomized ensemble approach for robust clustering across diverse datasets. Genome Biol 2024;25:242. [PMID: 39285487 PMCID: PMC11406744 DOI: 10.1186/s13059-024-03386-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 08/30/2024] [Indexed: 09/19/2024]  Open
7
Zhang K, Kan H, Mao A, Yu F, Geng L, Zhou T, Feng L, Ma X. Integrated Single-Cell Transcriptomic Atlas of Human Kidney Endothelial Cells. J Am Soc Nephrol 2024;35:578-593. [PMID: 38351505 PMCID: PMC11149048 DOI: 10.1681/asn.0000000000000320] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 02/09/2024] [Indexed: 03/23/2024]  Open
8
Feng M, Fei S, Zou J, Xia J, Lai W, Huang Y, Swevers L, Sun J. Single-Nucleus Sequencing of Silkworm Larval Brain Reveals the Key Role of Lysozyme in the Antiviral Immune Response in Brain Hemocytes. J Innate Immun 2024;16:173-187. [PMID: 38387449 PMCID: PMC10965234 DOI: 10.1159/000537815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/01/2024] [Indexed: 02/24/2024]  Open
9
Church SH, Mah JL, Wagner G, Dunn CW. Normalizing need not be the norm: count-based math for analyzing single-cell data. Theory Biosci 2024;143:45-62. [PMID: 37947999 DOI: 10.1007/s12064-023-00408-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023]
10
Carbonetto P, Luo K, Sarkar A, Hung A, Tayeb K, Pott S, Stephens M. GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. Genome Biol 2023;24:236. [PMID: 37858253 PMCID: PMC10588049 DOI: 10.1186/s13059-023-03067-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023]  Open
11
Mangiola S, Roth-Schulze AJ, Trussart M, Zozaya-Valdés E, Ma M, Gao Z, Rubin AF, Speed TP, Shim H, Papenfuss AT. sccomp: Robust differential composition and variability analysis for single-cell data. Proc Natl Acad Sci U S A 2023;120:e2203828120. [PMID: 37549298 PMCID: PMC10438834 DOI: 10.1073/pnas.2203828120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/18/2023] [Indexed: 08/09/2023]  Open
12
Xu Y, Kramann R, McCord RP, Hayat S. Fast model-free standardization and integration of single-cell transcriptomics data. RESEARCH SQUARE 2023:rs.3.rs-2485985. [PMID: 36747625 PMCID: PMC9901035 DOI: 10.21203/rs.3.rs-2485985/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
13
Li Z, Zhou X. BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies. Genome Biol 2022;23:168. [PMID: 35927760 PMCID: PMC9351148 DOI: 10.1186/s13059-022-02734-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/21/2022] [Indexed: 02/08/2023]  Open
14
Dave A, Nekritz E, Charytonowicz D, Beaumont M, Smith M, Beaumont K, Silva J, Sebra R. Integration of Single-Cell Transcriptomics With a High Throughput Functional Screening Assay to Resolve Cell Type, Growth Kinetics, and Stemness Heterogeneity Within the Comma-1D Cell Line. Front Genet 2022;13:894597. [PMID: 36630696 PMCID: PMC9237515 DOI: 10.3389/fgene.2022.894597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/20/2022] [Indexed: 01/14/2023]  Open
15
Cytotoxic innate lymphoid cells sense cancer cell-expressed interleukin-15 to suppress human and murine malignancies. Nat Immunol 2022;23:904-915. [PMID: 35618834 DOI: 10.1038/s41590-022-01213-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 04/14/2022] [Indexed: 12/15/2022]
16
Li L, Zhang Y, Ren Y, Cheng Z, Zhang Y, Wang X, Zhao H, Lu H. Pan-Cancer Single-Cell Analysis Reveals the Core Factors and Pathway in Specific Cancer Stem Cells of Upper Gastrointestinal Cancer. Front Bioeng Biotechnol 2022;10:849798. [PMID: 35646860 PMCID: PMC9136039 DOI: 10.3389/fbioe.2022.849798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/07/2022] [Indexed: 12/24/2022]  Open
17
Yu L, Cao Y, Yang JYH, Yang P. Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data. Genome Biol 2022;23:49. [PMID: 35135612 PMCID: PMC8822786 DOI: 10.1186/s13059-022-02622-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/27/2022] [Indexed: 01/24/2023]  Open
18
Lotfollahi M, Naghipourfar M, Luecken MD, Khajavi M, Büttner M, Wagenstetter M, Avsec Ž, Gayoso A, Yosef N, Interlandi M, Rybakov S, Misharin AV, Theis FJ. Mapping single-cell data to reference atlases by transfer learning. Nat Biotechnol 2022;40:121-130. [PMID: 34462589 PMCID: PMC8763644 DOI: 10.1038/s41587-021-01001-7] [Citation(s) in RCA: 233] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 06/28/2021] [Indexed: 02/07/2023]
19
Mazan-Mamczarz K, Ha J, De S, Sen P. Single-Cell Analysis of the Transcriptome and Epigenome. Methods Mol Biol 2022;2399:21-60. [PMID: 35604552 PMCID: PMC9352558 DOI: 10.1007/978-1-0716-1831-8_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
20
You Y, Tian L, Su S, Dong X, Jabbari JS, Hickey PF, Ritchie ME. Benchmarking UMI-based single-cell RNA-seq preprocessing workflows. Genome Biol 2021;22:339. [PMID: 34906205 PMCID: PMC8672463 DOI: 10.1186/s13059-021-02552-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022]  Open
21
Bej S, Galow AM, David R, Wolfien M, Wolkenhauer O. Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling. BMC Bioinformatics 2021;22:557. [PMID: 34798805 PMCID: PMC8603509 DOI: 10.1186/s12859-021-04469-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/03/2021] [Indexed: 11/10/2022]  Open
22
Zappia L, Theis FJ. Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape. Genome Biol 2021;22:301. [PMID: 34715899 PMCID: PMC8555270 DOI: 10.1186/s13059-021-02519-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022]  Open
23
Transcriptional Differences in Lipid-Metabolizing Enzymes in Murine Sebocytes Derived from Sebaceous Glands of the Skin and Preputial Glands. Int J Mol Sci 2021;22:ijms222111631. [PMID: 34769061 PMCID: PMC8584257 DOI: 10.3390/ijms222111631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/18/2022]  Open
24
Shiga M, Seno S, Onizuka M, Matsuda H. SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization. PeerJ 2021;9:e12087. [PMID: 34532161 PMCID: PMC8404576 DOI: 10.7717/peerj.12087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/07/2021] [Indexed: 11/20/2022]  Open
25
Schmidt F, Ranjan B, Lin Q, Krishnan V, Joanito I, Honardoost M, Nawaz Z, Venkatesh P, Tan J, Rayan N, Ong S, Prabhakar S. RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data. Nucleic Acids Res 2021;49:8505-8519. [PMID: 34320202 PMCID: PMC8344557 DOI: 10.1093/nar/gkab632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 11/13/2022]  Open
26
Talukdar S, Chang Z, Winterhoff B, Starr TK. Single-Cell RNA Sequencing of Ovarian Cancer: Promises and Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021;1330:113-123. [PMID: 34339033 DOI: 10.1007/978-3-030-73359-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
27
Wilk AJ, Lee MJ, Wei B, Parks B, Pi R, Martínez-Colón GJ, Ranganath T, Zhao NQ, Taylor S, Becker W, Stanford COVID-19 Biobank, Jimenez-Morales D, Blomkalns AL, O’Hara R, Ashley EA, Nadeau KC, Yang S, Holmes S, Rabinovitch M, Rogers AJ, Greenleaf WJ, Blish CA. Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19. J Exp Med 2021;218:e20210582. [PMID: 34128959 PMCID: PMC8210586 DOI: 10.1084/jem.20210582] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 12/20/2022]  Open
28
Song D, Li K, Hemminger Z, Wollman R, Li JJ. scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling. Bioinformatics 2021;37:i358-i366. [PMID: 34252925 PMCID: PMC8275345 DOI: 10.1093/bioinformatics/btab273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
29
Wang Q, Peng C, Yang M, Huang F, Duan X, Wang S, Cheng H, Yang H, Zhao H, Qin Q. Single-cell RNA-seq landscape midbrain cell responses to red spotted grouper nervous necrosis virus infection. PLoS Pathog 2021;17:e1009665. [PMID: 34185811 PMCID: PMC8241073 DOI: 10.1371/journal.ppat.1009665] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022]  Open
30
Human intermediate progenitor diversity during cortical development. Proc Natl Acad Sci U S A 2021;118:2019415118. [PMID: 34155100 DOI: 10.1073/pnas.2019415118] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
31
Li L, Xiong F, Wang Y, Zhang S, Gong Z, Li X, He Y, Shi L, Wang F, Liao Q, Xiang B, Zhou M, Li X, Li Y, Li G, Zeng Z, Xiong W, Guo C. What are the applications of single-cell RNA sequencing in cancer research: a systematic review. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021;40:163. [PMID: 33975628 PMCID: PMC8111731 DOI: 10.1186/s13046-021-01955-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022]
32
Krishna C, DiNatale RG, Kuo F, Srivastava RM, Vuong L, Chowell D, Gupta S, Vanderbilt C, Purohit TA, Liu M, Kansler E, Nixon BG, Chen YB, Makarov V, Blum KA, Attalla K, Weng S, Salmans ML, Golkaram M, Liu L, Zhang S, Vijayaraghavan R, Pawlowski T, Reuter V, Carlo MI, Voss MH, Coleman J, Russo P, Motzer RJ, Li MO, Leslie CS, Chan TA, Hakimi AA. Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy. Cancer Cell 2021;39:662-677.e6. [PMID: 33861994 PMCID: PMC8268947 DOI: 10.1016/j.ccell.2021.03.007] [Citation(s) in RCA: 229] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 01/18/2021] [Accepted: 03/22/2021] [Indexed: 02/08/2023]
33
Marques L, Lontra P, Wanke P, Antunes JJM. Governance modes in supply chains and financial performance at buyer, supplier and dyadic levels: the positive impact of power balance. BENCHMARKING-AN INTERNATIONAL JOURNAL 2021. [DOI: 10.1108/bij-03-2020-0114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
34
Al Mahi N, Zhang EY, Sherman S, Yu JJ, Medvedovic M. Connectivity Map Analysis of a Single-Cell RNA-Sequencing -Derived Transcriptional Signature of mTOR Signaling. Int J Mol Sci 2021;22:ijms22094371. [PMID: 33922083 PMCID: PMC8122562 DOI: 10.3390/ijms22094371] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022]  Open
35
Benchmarking mass spectrometry based proteomics algorithms using a simulated database. ACTA ACUST UNITED AC 2021;10. [PMID: 34012763 DOI: 10.1007/s13721-021-00298-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
36
Do VH, Rojas Ringeling F, Canzar S. Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data. Genome Res 2021;31:677-688. [PMID: 33627473 PMCID: PMC8015854 DOI: 10.1101/gr.267906.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 02/19/2021] [Indexed: 12/25/2022]
37
Liu HL, Wang YN, Feng SY. Brain tumors: Cancer stem-like cells interact with tumor microenvironment. World J Stem Cells 2020;12:1439-1454. [PMID: 33505594 PMCID: PMC7789119 DOI: 10.4252/wjsc.v12.i12.1439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 10/07/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023]  Open
38
Dimitrov D, Gu Q. BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis. PeerJ 2020;8:e10469. [PMID: 33391870 PMCID: PMC7761193 DOI: 10.7717/peerj.10469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022]  Open
39
Andrews TS, Kiselev VY, McCarthy D, Hemberg M. Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data. Nat Protoc 2020;16:1-9. [PMID: 33288955 DOI: 10.1038/s41596-020-00409-w] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 09/08/2020] [Indexed: 01/01/2023]
40
Augsornworawat P, Millman JR. Single-cell RNA sequencing for engineering and studying human islets. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2020;16:27-33. [PMID: 33738370 PMCID: PMC7963276 DOI: 10.1016/j.cobme.2020.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Crowell HL, Soneson C, Germain PL, Calini D, Collin L, Raposo C, Malhotra D, Robinson MD. muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data. Nat Commun 2020;11:6077. [PMID: 33257685 PMCID: PMC7705760 DOI: 10.1038/s41467-020-19894-4] [Citation(s) in RCA: 232] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023]  Open
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Mohanraj S, Díaz-Mejía JJ, Pham MD, Elrick H, Husić M, Rashid S, Luo P, Bal P, Lu K, Patel S, Mahalanabis A, Naidas A, Christensen E, Croucher D, Richards LM, Shooshtari P, Brudno M, Ramani AK, Pugh TJ. CReSCENT: CanceR Single Cell ExpressioN Toolkit. Nucleic Acids Res 2020;48:W372-W379. [PMID: 32479601 PMCID: PMC7319570 DOI: 10.1093/nar/gkaa437] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/28/2020] [Accepted: 05/12/2020] [Indexed: 01/10/2023]  Open
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Zhao X, Wu S, Fang N, Sun X, Fan J. Evaluation of single-cell classifiers for single-cell RNA sequencing data sets. Brief Bioinform 2020;21:1581-1595. [PMID: 31675098 PMCID: PMC7947964 DOI: 10.1093/bib/bbz096] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/06/2019] [Accepted: 07/08/2019] [Indexed: 12/19/2022]  Open
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Wang X, Sun Z, Zhang Y, Xu Z, Xin H, Huang H, Duerr RH, Chen K, Ding Y, Chen W. BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data. Nucleic Acids Res 2020;48:5814-5824. [PMID: 32379315 PMCID: PMC7293045 DOI: 10.1093/nar/gkaa314] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/17/2020] [Accepted: 04/20/2020] [Indexed: 12/25/2022]  Open
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Germain PL, Sonrel A, Robinson MD. pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools. Genome Biol 2020;21:227. [PMID: 32873325 PMCID: PMC7465801 DOI: 10.1186/s13059-020-02136-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/06/2020] [Indexed: 11/13/2022]  Open
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Kim TH, Zhou X, Chen M. Demystifying "drop-outs" in single-cell UMI data. Genome Biol 2020;21:196. [PMID: 32762710 PMCID: PMC7412673 DOI: 10.1186/s13059-020-02096-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/08/2020] [Indexed: 01/10/2023]  Open
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Chen L, Zhai Y, He Q, Wang W, Deng M. Integrating Deep Supervised, Self-Supervised and Unsupervised Learning for Single-Cell RNA-seq Clustering and Annotation. Genes (Basel) 2020;11:E792. [PMID: 32674393 PMCID: PMC7397036 DOI: 10.3390/genes11070792] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/29/2020] [Accepted: 07/08/2020] [Indexed: 12/31/2022]  Open
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Wilk AJ, Rustagi A, Zhao NQ, Roque J, Martínez-Colón GJ, McKechnie JL, Ivison GT, Ranganath T, Vergara R, Hollis T, Simpson LJ, Grant P, Subramanian A, Rogers AJ, Blish CA. A single-cell atlas of the peripheral immune response in patients with severe COVID-19. Nat Med 2020;26:1070-1076. [PMID: 32514174 PMCID: PMC7382903 DOI: 10.1038/s41591-020-0944-y] [Citation(s) in RCA: 1134] [Impact Index Per Article: 226.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/19/2020] [Indexed: 02/08/2023]
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Hou R, Denisenko E, Forrest ARR. scMatch: a single-cell gene expression profile annotation tool using reference datasets. Bioinformatics 2020;35:4688-4695. [PMID: 31028376 PMCID: PMC6853649 DOI: 10.1093/bioinformatics/btz292] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/28/2019] [Accepted: 04/21/2019] [Indexed: 12/17/2022]  Open
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Lin Y, Cao Y, Kim HJ, Salim A, Speed TP, Lin DM, Yang P, Yang JYH. scClassify: sample size estimation and multiscale classification of cells using single and multiple reference. Mol Syst Biol 2020;16:e9389. [PMID: 32567229 PMCID: PMC7306901 DOI: 10.15252/msb.20199389] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022]  Open
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