RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR [version 2; referees: 3 approved]

by Charity W. Law, Monther Alhamdoosh, Shian Su, Gordon K. Smyth, Matthew E. Ritchie
Published 2016-11-01

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR [version 1; referees: 3 approved]

by Charity W. Law, Monther Alhamdoosh, Shian Su, Gordon K. Smyth, Matthew E. Ritchie
Published 2016-06-01

Easy and efficient ensemble gene set testing with EGSEA [version 1; referees: 1 approved, 3 approved with reservations]

by Monther Alhamdoosh, Charity W. Law, Luyi Tian, Julie M. Sheridan, Milica Ng, Matthew E. Ritchie
Published 2017-11-01

A guide to creating design matrices for gene expression experiments [version 1; peer review: 2 approved]

by Charity W. Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, Gordon K. Smyth, Matthew E. Ritchie
Published 2020-12-01

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR [version 3; referees: 3 approved]

by Charity W. Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi Tian, Gordon K. Smyth, Matthew E. Ritchie
Published 2018-12-01

Whole blood transcriptomics reveals granulocyte colony‐stimulating factor as a mediator of cardiopulmonary bypass‐induced systemic inflammatory response syndrome

by Katherine R Martin, Cristina Gamell, Tsin Yee Tai, Roberto Bonelli, Jacinta Hansen, James Tatoulis, Monther Alhamdoosh, Nicholas Wilson, Ian Wicks
Published 2024-01-01

Machine learning applied to whole‐blood RNA‐sequencing data uncovers distinct subsets of patients with systemic lupus erythematosus

by William A Figgett, Katherine Monaghan, Milica Ng, Monther Alhamdoosh, Eugene Maraskovsky, Nicholas J Wilson, Alberta Y Hoi, Eric F Morand, Fabienne Mackay
Published 2019-01-01

Publisher Correction: Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data

by Yue You, Xueyi Dong, Yong Kiat Wee, Mhairi J. Maxwell, Monther Alhamdoosh, Gordon K. Smyth, Peter F. Hickey, Matthew E. Ritchie, Charity W. Law
Published 2023-05-01

Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data

by Yue You, Xueyi Dong, Yong Kiat Wee, Mhairi J. Maxwell, Monther Alhamdoosh, Gordon K. Smyth, Peter F. Hickey, Matthew E. Ritchie, Charity W. Law
Published 2023-05-01

Matrix metalloproteinase-7 is increased in lung bases but not apices in idiopathic pulmonary fibrosis

by Jade Jaffar, Mae Wong, Gregory A. Fishbein, Monther Alhamdoosh, Laura McMillan, Cristina Gamell-Fulla, Milica Ng, Nick Wilson, Karen Symons, Ian Glaspole, Glen Westall
Published 2022-10-01

Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved]

by Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez, Neil Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla Garcia, Josep Ll. Gelpí, Simon Gladman, Carole Goble, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C. Griffin, Björn Grüning, Jonas Hagberg, Petr Holub, Rob Hooft, Jon Ison, Daniel S. Katz, Brane Leskošek, Federico López Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola Mulder, Yasset Perez-Riverol, Robert Pergl, Horst Pichler, Bernard Pope, Ferran Sanz, Maria V. Schneider, Victoria Stodden, Radosław Suchecki, Radka Svobodová Vařeková, Harry-Anton Talvik, Ilian Todorov, Andrew Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch
Published 2017-06-01