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For: Prieto C, Barrios D, Villaverde A. SingleCAnalyzer: Interactive Analysis of Single Cell RNA-Seq Data on the Cloud. Front Bioinform 2022;2:793309. [PMID: 36304292 PMCID: PMC9580930 DOI: 10.3389/fbinf.2022.793309] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/09/2022] [Indexed: 12/13/2022]  Open
Number Cited by Other Article(s)
1
Ferrena A, Zheng XY, Jackson K, Hoang B, Morrow BE, Zheng D. scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison. NAR Genom Bioinform 2024;6:lqae134. [PMID: 39345754 PMCID: PMC11437360 DOI: 10.1093/nargab/lqae134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/07/2024] [Accepted: 09/18/2024] [Indexed: 10/01/2024]  Open
2
Yarlagadda S, Giorgio TD. A guide to single-cell RNA sequencing analysis using web-based tools for non-bioinformatician. FEBS J 2024;291:2545-2561. [PMID: 38148322 DOI: 10.1111/febs.17036] [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: 10/12/2023] [Accepted: 12/14/2023] [Indexed: 12/28/2023]
3
Wei W, Xia X, Li T, Chen Q, Feng X. Shaoxia: a web-based interactive analysis platform for single cell RNA sequencing data. BMC Genomics 2024;25:402. [PMID: 38658838 PMCID: PMC11040744 DOI: 10.1186/s12864-024-10322-1] [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: 01/09/2024] [Accepted: 04/18/2024] [Indexed: 04/26/2024]  Open
4
Islam MT, Liu Y, Hassan MM, Abraham PE, Merlet J, Townsend A, Jacobson D, Buell CR, Tuskan GA, Yang X. Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology. BIODESIGN RESEARCH 2024;6:0029. [PMID: 38435807 PMCID: PMC10905259 DOI: 10.34133/bdr.0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/28/2024] [Indexed: 03/05/2024]  Open
5
Klamann C, Lau CJ, Ruiz-Ramírez J, Schwartz GW. TooManyCellsInteractive: A visualization tool for dynamic exploration of single-cell data. Gigascience 2024;13:giae056. [PMID: 39172544 PMCID: PMC11340645 DOI: 10.1093/gigascience/giae056] [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: 12/13/2023] [Revised: 05/27/2024] [Accepted: 07/15/2024] [Indexed: 08/24/2024]  Open
6
Nouri N, Kurlovs AH, Gaglia G, de Rinaldis E, Savova V. Scaling up single-cell RNA-seq data analysis with CellBridge workflow. Bioinformatics 2023;39:btad760. [PMID: 38113416 PMCID: PMC10751228 DOI: 10.1093/bioinformatics/btad760] [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: 07/31/2023] [Revised: 12/04/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023]  Open
7
Pan L, Mou T, Huang Y, Hong W, Yu M, Li X. Ursa: A Comprehensive Multiomics Toolbox for High-Throughput Single-Cell Analysis. Mol Biol Evol 2023;40:msad267. [PMID: 38091963 PMCID: PMC10752348 DOI: 10.1093/molbev/msad267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/08/2023] [Accepted: 11/03/2023] [Indexed: 12/28/2023]  Open
8
Tzaferis C, Karatzas E, Baltoumas FA, Pavlopoulos GA, Kollias G, Konstantopoulos D. SCALA: A complete solution for multimodal analysis of single-cell Next Generation Sequencing data. Comput Struct Biotechnol J 2023;21:5382-5393. [PMID: 38022693 PMCID: PMC10651449 DOI: 10.1016/j.csbj.2023.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]  Open
9
Landais Y, Vallot C. Multi-modal quantification of pathway activity with MAYA. Nat Commun 2023;14:1668. [PMID: 36966153 PMCID: PMC10039856 DOI: 10.1038/s41467-023-37410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/16/2023] [Indexed: 03/27/2023]  Open
10
Umu SU, Rapp Vander-Elst K, Karlsen VT, Chouliara M, Bækkevold ES, Jahnsen FL, Domanska D. Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis. Gigascience 2022;12:giad091. [PMID: 37889009 PMCID: PMC10603768 DOI: 10.1093/gigascience/giad091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/25/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023]  Open
11
Mikolajewicz N, Gacesa R, Aguilera-Uribe M, Brown KR, Moffat J, Han H. Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline. Commun Biol 2022;5:1142. [PMID: 36307536 PMCID: PMC9616830 DOI: 10.1038/s42003-022-04093-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/11/2022] [Indexed: 11/08/2022]  Open
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