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A single-cell RNA-sequencing training and analysis suite using the Galaxy framework.
Tekman M, Batut B, Ostrovsky A, Antoniewski C, Clements D, Ramirez F, Etherington GJ, Hotz HR, Scholtalbers J, Manning JR, Bellenger L, Doyle MA, Heydarian M, Huang N, Soranzo N, Moreno P, Mautner S, Papatheodorou I, Nekrutenko A, Taylor J, Blankenberg D, Backofen R, Grüning B. Tekman M, et al. Among authors: ramirez f. Gigascience. 2020 Oct 20;9(10):giaa102. doi: 10.1093/gigascience/giaa102. Gigascience. 2020. PMID: 33079170 Free PMC article.
Community-Driven Data Analysis Training for Biology.
Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D; Galaxy Training Network; Taylor J, Backofen R, Nekrutenko A, Grüning B. Batut B, et al. Among authors: ramirez f. Cell Syst. 2018 Jun 27;6(6):752-758.e1. doi: 10.1016/j.cels.2018.05.012. Cell Syst. 2018. PMID: 29953864 Free PMC article.
pyGenomeTracks: reproducible plots for multivariate genomic datasets.
Lopez-Delisle L, Rabbani L, Wolff J, Bhardwaj V, Backofen R, Grüning B, Ramírez F, Manke T. Lopez-Delisle L, et al. Among authors: ramirez f. Bioinformatics. 2021 Apr 20;37(3):422-423. doi: 10.1093/bioinformatics/btaa692. Bioinformatics. 2021. PMID: 32745185 Free PMC article.
deepTools: a flexible platform for exploring deep-sequencing data.
Ramírez F, Dündar F, Diehl S, Grüning BA, Manke T. Ramírez F, et al. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W187-91. doi: 10.1093/nar/gku365. Epub 2014 May 5. Nucleic Acids Res. 2014. PMID: 24799436 Free PMC article.
MOF-associated complexes ensure stem cell identity and Xist repression.
Chelmicki T, Dündar F, Turley MJ, Khanam T, Aktas T, Ramírez F, Gendrel AV, Wright PR, Videm P, Backofen R, Heard E, Manke T, Akhtar A. Chelmicki T, et al. Among authors: ramirez f. Elife. 2014 May 19;3:e02024. doi: 10.7554/eLife.02024. Elife. 2014. PMID: 24842875 Free PMC article.
1,109 results