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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: doyle ma. Gigascience. 2020 Oct 20;9(10):giaa102. doi: 10.1093/gigascience/giaa102. Gigascience. 2020. PMID: 33079170 Free PMC article.
The RNA workbench 2.0: next generation RNA data analysis.
Fallmann J, Videm P, Bagnacani A, Batut B, Doyle MA, Klingstrom T, Eggenhofer F, Stadler PF, Backofen R, Grüning B. Fallmann J, et al. Among authors: doyle ma. Nucleic Acids Res. 2019 Jul 2;47(W1):W511-W515. doi: 10.1093/nar/gkz353. Nucleic Acids Res. 2019. PMID: 31073612 Free PMC article.
User-friendly, scalable tools and workflows for single-cell RNA-seq analysis.
Moreno P, Huang N, Manning JR, Mohammed S, Solovyev A, Polanski K, Bacon W, Chazarra R, Talavera-López C, Doyle MA, Marnier G, Grüning B, Rasche H, George N, Fexova SK, Alibi M, Miao Z, Perez-Riverol Y, Haeussler M, Brazma A, Teichmann S, Meyer KB, Papatheodorou I. Moreno P, et al. Among authors: doyle ma. Nat Methods. 2021 Apr;18(4):327-328. doi: 10.1038/s41592-021-01102-w. Nat Methods. 2021. PMID: 33782609 Free PMC article. No abstract available.
RNA-Seq Data Analysis in Galaxy.
Batut B, van den Beek M, Doyle MA, Soranzo N. Batut B, et al. Among authors: doyle ma. Methods Mol Biol. 2021;2284:367-392. doi: 10.1007/978-1-0716-1307-8_20. Methods Mol Biol. 2021. PMID: 33835453
Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment.
Li J, Doyle MA, Saeed I, Wong SQ, Mar V, Goode DL, Caramia F, Doig K, Ryland GL, Thompson ER, Hunter SM, Halgamuge SK, Ellul J, Dobrovic A, Campbell IG, Papenfuss AT, McArthur GA, Tothill RW. Li J, et al. Among authors: doyle ma. PLoS One. 2014 Apr 21;9(4):e95217. doi: 10.1371/journal.pone.0095217. eCollection 2014. PLoS One. 2014. PMID: 24752294 Free PMC article.
Interfacing Seurat with the R tidy universe.
Mangiola S, Doyle MA, Papenfuss AT. Mangiola S, et al. Among authors: doyle ma. Bioinformatics. 2021 Nov 18;37(22):4100-4107. doi: 10.1093/bioinformatics/btab404. Bioinformatics. 2021. PMID: 34028547 Free PMC article.
CONTRA: copy number analysis for targeted resequencing.
Li J, Lupat R, Amarasinghe KC, Thompson ER, Doyle MA, Ryland GL, Tothill RW, Halgamuge SK, Campbell IG, Gorringe KL. Li J, et al. Among authors: doyle ma. Bioinformatics. 2012 May 15;28(10):1307-13. doi: 10.1093/bioinformatics/bts146. Epub 2012 Apr 2. Bioinformatics. 2012. PMID: 22474122 Free PMC article.
127 results