M
Matthew E. Ritchie
Researcher at Walter and Eliza Hall Institute of Medical Research
Publications - 155
Citations - 31733
Matthew E. Ritchie is an academic researcher from Walter and Eliza Hall Institute of Medical Research. The author has contributed to research in topics: Bioconductor & Biology. The author has an hindex of 42, co-authored 135 publications receiving 20980 citations. Previous affiliations of Matthew E. Ritchie include University of Cambridge & University of Melbourne.
Papers
More filters
Journal ArticleDOI
limma powers differential expression analyses for RNA-sequencing and microarray studies
Matthew E. Ritchie,Belinda Phipson,Di Wu,Yifang Hu,Charity W. Law,Wei Shi,Gordon K. Smyth,Gordon K. Smyth +7 more
TL;DR: The philosophy and design of the limma package is reviewed, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
Journal ArticleDOI
Opportunities and challenges in long-read sequencing data analysis.
Shanika L. Amarasinghe,Shanika L. Amarasinghe,Shian Su,Shian Su,Xueyi Dong,Xueyi Dong,Luke Zappia,Matthew E. Ritchie,Matthew E. Ritchie,Quentin Gouil,Quentin Gouil +10 more
TL;DR: The current landscape of available tools is reviewed, the principles of error correction, base modification detection, and long-read transcriptomics analysis are focused on, and the challenges that remain are highlighted.
Journal ArticleDOI
A comparison of background correction methods for two-colour microarrays
Matthew E. Ritchie,Jeremy D. Silver,Alicia Oshlack,Melissa L. Holmes,Dileepa Diyagama,Andrew J. Holloway,Gordon K. Smyth +6 more
TL;DR: The model-based correction methods are shown to be markedly superior to the usual practice of subtracting local background estimates, and methods which stabilize the variances of the log-ratios along the intensity range perform the best.
Journal ArticleDOI
Apoptotic Caspases Suppress mtDNA-Induced STING-Mediated Type I IFN Production
Michael J. White,Michael J. White,Kate McArthur,Kate McArthur,Donald Metcalf,Donald Metcalf,Rachael M. Lane,John C. Cambier,Marco J Herold,Marco J Herold,Mark F. van Delft,Mark F. van Delft,Sammy Bedoui,Guillaume Lessene,Guillaume Lessene,Matthew E. Ritchie,Matthew E. Ritchie,David C.S. Huang,David C.S. Huang,Benjamin T. Kile,Benjamin T. Kile +20 more
TL;DR: The apoptotic caspase cascade functions to render mitochondrial apoptosis immunologically silent, and suppresses type I interferon (IFN) production by cells undergoing Bak/Bax-mediated apoptosis.
Journal ArticleDOI
beadarray: R classes and methods for Illumina bead-based data.
TL;DR: The R/Bioconductor package beadarray allows raw data from Illumina experiments to be read and stored in convenient R classes and users are free to choose between various methods of image processing, background correction and normalization in their analysis rather than using the defaults in Illumina's; proprietary software.