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A scalable SCENIC workflow for single-cell gene regulatory network analysis.
Van de Sande B, Flerin C, Davie K, De Waegeneer M, Hulselmans G, Aibar S, Seurinck R, Saelens W, Cannoodt R, Rouchon Q, Verbeiren T, De Maeyer D, Reumers J, Saeys Y, Aerts S. Van de Sande B, et al. Among authors: flerin c. Nat Protoc. 2020 Jul;15(7):2247-2276. doi: 10.1038/s41596-020-0336-2. Epub 2020 Jun 19. Nat Protoc. 2020. PMID: 32561888
Systematic benchmarking of single-cell ATAC-sequencing protocols.
De Rop FV, Hulselmans G, Flerin C, Soler-Vila P, Rafels A, Christiaens V, González-Blas CB, Marchese D, Caratù G, Poovathingal S, Rozenblatt-Rosen O, Slyper M, Luo W, Muus C, Duarte F, Shrestha R, Bagdatli ST, Corces MR, Mamanova L, Knights A, Meyer KB, Mulqueen R, Taherinasab A, Maschmeyer P, Pezoldt J, Lambert CLG, Iglesias M, Najle SR, Dossani ZY, Martelotto LG, Burkett Z, Lebofsky R, Martin-Subero JI, Pillai S, Sebé-Pedrós A, Deplancke B, Teichmann SA, Ludwig LS, Braun TP, Adey AC, Greenleaf WJ, Buenrostro JD, Regev A, Aerts S, Heyn H. De Rop FV, et al. Among authors: flerin c. Nat Biotechnol. 2023 Aug 3. doi: 10.1038/s41587-023-01881-x. Online ahead of print. Nat Biotechnol. 2023. PMID: 37537502