Maria Doyle

Galaxy Training: A powerful framework for teaching!

Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel Blankenberg, Pratik D Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J Griffin, Coline Royaux, Yvan Le Bras, Subina Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi Bacon, Fotis Psomopoulos, et al.

Journal article  |  2023  |  PLoS Comput Biol

There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of..

Interfacing Seurat with the R tidy universe

Stefano Mangiola, Maria A Doyle, Anthony T Papenfuss

Journal article  |  2021  |  BIOINFORMATICS

MOTIVATION: Seurat is one of the most popular software suites for the analysis of single-cell RNA sequencing data. Considering the..

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis

Pablo Moreno, Ni Huang, Jonathan R Manning, Suhaib Mohammed, Andrey Solovyev, Krzysztof Polanski, Wendi Bacon, Ruben Chazarra, Carlos Talavera-Lopez, Maria A Doyle, Guilhem Marnier, Bjoern Gruening, Helena Rasche, Nancy George, Silvie Korena Fexova, Mohamed Alibi, Zhichao Miao, Yasset Perez-Riverol, Maximilian Haeussler, Alvis Brazma, et al.

Journal article  |  2021  |  NATURE METHODS

tidybulk: an R tidy framework for modular transcriptomic data analysis

Stefano Mangiola, Ramyar Molania, Ruining Dong, Maria A Doyle, Anthony T Papenfuss

Journal article  |  2021  |  GENOME BIOLOGY

Recently, efforts have been made toward the harmonization of transcriptomic data structures and workflows using the concept of dat..

RNA-Seq Data Analysis in Galaxy

Berenice Batut, Marius van den Beek, Maria A Doyle, Nicola Soranzo

Book Chapter  |  2021  |  Methods in Molecular Biology

A complete RNA-Seq analysis involves the use of several different tools, with substantial software and computational requirements...

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Mehmet Tekman, Berenice Batut, Alexander Ostrovsky, Christophe Antoniewski, Dave Clements, Fidel Ramirez, Graham J Etherington, Hans-Rudolf Hotz, Jelle Scholtalbers, Jonathan R Manning, Lea Bellenger, Maria A Doyle, Mohammad Heydarian, Ni Huang, Nicola Soranzo, Pablo Moreno, Stefan Mautner, Irene Papatheodorou, Anton Nekrutenko, James Taylor, et al.

Journal article  |  2020  |  GIGASCIENCE

BACKGROUND: The vast ecosystem of single-cell RNA-sequencing tools has until recently been plagued by an excess of diverging analy..

Molecular comparison of pure ovarian fibroma with serous benign ovarian tumours

Sally M Hunter, Genevieve V Dall, Maria A Doyle, Richard Lupat, Jason Li, Prue Allan, Simone M Rowley, David Bowtell, Ian G Campbell, Kylie L Gorringe

Journal article  |  2020  |  BMC RESEARCH NOTES

OBJECTIVE: Ovarian fibromas and adenofibromas are rare ovarian tumours. They are benign tumours composed of spindle-like stromal c..

Germline whole exome sequencing of a family with appendiceal mucinous tumours presenting with pseudomyxoma peritonei

Mei Sim Lung, Catherine A Mitchell, Maria A Doyle, Andrew C Lynch, Kylie L Gorringe, David DL Bowtell, Ian G Campbell, Alison H Trainer

Journal article  |  2020  |  BMC CANCER

BACKGROUND: Familial cases of appendiceal mucinous tumours (AMTs) are extremely rare and the underlying genetic aetiology uncertai..

CDK13 cooperates with CDK12 to control global RNA polymerase II processivity

Zheng Fan, Jennifer R Devlin, Simon J Hogg, Maria A Doyle, Paul F Harrison, Izabela Todorovski, Leonie A Cluse, Deborah A Knight, Jarrod J Sandow, Gareth Gregory, Andrew Fox, Traude H Beilharz, Nicholas Kwiatkowski, Nichollas E Scott, Ana Tufegdzic Vidakovic, Gavin P Kelly, Jesper Q Svejstrup, Matthias Geyer, Nathanael S Gray, Stephin J Vervoort, et al.

Journal article  |  2020  |  SCIENCE ADVANCES

The RNA polymerase II (POLII)-driven transcription cycle is tightly regulated at distinct checkpoints by cyclin-dependent kinases ..

The RNA workbench 2.0: next generation RNA data analysis

Joerg Fallmann, Pavankumar Videm, Andrea Bagnacani, Berenice Batut, Maria A Doyle, Tomas Klingstrom, Florian Eggenhofer, Peter F Stadler, Rolf Backofen, Bjoern Gruening

Journal article  |  2019  |  NUCLEIC ACIDS RESEARCH

RNA has become one of the major research topics in molecular biology. As a central player in key processes regulating gene express..