Empirical array quality weights in the analysis of microarray data. - Matthew E. Ritchie; Dileepa S. Diyagama; Jody Neilson; Ryan van Laar; Alexander Dobrovic; Andrew J. Holloway; Gordon K. Smyth (BMC Bioinform., 2006)

beadarray: R classes and methods for Illumina bead-based data. - Mark J. Dunning; Mike L. Smith; Matthew E. Ritchie; Simon Tavaré (Bioinform., 2007)

A comparison of background correction methods for two-colour microarrays. - Matthew E. Ritchie; Jeremy David Silver; Alicia Oshlack; Melissa Holmes; Dileepa S. Diyagama; Andrew J. Holloway; Gordon K. Smyth (Bioinform., 2007)

BASH: a tool for managing BeadArray spatial artefacts. - Jonathan M. Cairns; Mark J. Dunning; Matthew E. Ritchie; Roslin Russell; Andy G. Lynch (Bioinform., 2008)

Statistical issues in the analysis of Illumina data. - Mark J. Dunning; Nuno L. Barbosa-Morais; Andy G. Lynch; Simon Tavaré; Matthew E. Ritchie (BMC Bioinform., 2008)

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. - Matthew E. Ritchie; Benilton S. Carvalho; Kurt N. Hetrick; Simon Tavaré; Rafael A. Irizarry (Bioinform., 2009)

Swift: primary data analysis for the Illumina Solexa sequencing platform. - Nava Whiteford; Tom Skelly; Christina Curtis; Matthew E. Ritchie; Andrea Löhr; Alexander Wait Zaranek; Irina I. Abnizova; Clive Brown (Bioinform., 2009)

Illumina WG-6 BeadChip strips should be normalized separately. - Wei Shi; Ashish Banerjee; Matthew E. Ritchie; Steve Gerondakis; Gordon K. Smyth (BMC Bioinform., 2009)

Data analysis issues for allele-specific expression using Illumina's GoldenGate assay. - Matthew E. Ritchie; Matthew S. Forrest; Antigone S. Dimas; Caroline Daelemans; Emmanouil T. Dermitzakis; Panagiotis Deloukas; Simon Tavaré (BMC Bioinform., 2010)

Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips. - Matthew E. Ritchie; Ruijie Liu; Benilton S. Carvalho; Rafael A. Irizarry (BMC Bioinform., 2011)

BeadArray Expression Analysis Using Bioconductor. - Matthew E. Ritchie; Mark J. Dunning; Mike L. Smith; Wei Shi; Andy G. Lynch (PLoS Comput. Biol., 2011)

Allele-specific expression analysis methods for high-density SNP microarray data. - Ruijie Liu; Ana-Teresa Maia; Roslin Russell; Carlos Caldas; Bruce A. Ponder; Matthew E. Ritchie (Bioinform., 2012)

illuminaio: An open source IDAT parsing tool for Illumina microarrays. - Mike L. Smith; Keith A. Baggerly; Henrik Bengtsson; Matthew E. Ritchie; Kasper D. Hansen (F1000Research, 2013)

KRLMM: an adaptive genotype calling method for common and low frequency variants. - Ruijie Liu; Zhiyin Dai; Meredith Yeager; Rafael A. Irizarry; Matthew E. Ritchie (BMC Bioinform., 2014)

Combining multiple tools outperforms individual methods in gene set enrichment analyses. - Monther Alhamdoosh; Milica Ng; Nicholas J. Wilson; Julie M. Sheridan; Huy Huynh; Michael J. Wilson; Matthew E. Ritchie (Bioinform., 2017)

Glimma: interactive graphics for gene expression analysis. - Shian Su; Charity W. Law; Casey Ah-Cann; Marie-Liesse Asselin-Labat; Marnie E. Blewitt; Matthew E. Ritchie (Bioinform., 2017)

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data. - Luyi Tian; Shian Su; Xueyi Dong; Daniela Amann-Zalcenstein; Christine Biben; Azadeh Seidi; Douglas J. Hilton; Shalin H. Naik; Matthew E. Ritchie (PLoS Comput. Biol., 2018)

BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem. - Shian Su; Vincent J. Carey; Lori A. Shepherd; Matthew E. Ritchie; Martin T. Morgan; Sean Davis 001 (F1000Research, 2019)

CellBench: R/Bioconductor software for comparing single-cell RNA-seq analysis methods. - Shian Su; Luyi Tian; Xueyi Dong; Peter F. Hickey; Saskia Freytag; Matthew E. Ritchie (Bioinform., 2020)

NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data. - Shian Su; Quentin Gouil; Marnie E. Blewitt; Dianne Cook; Peter F. Hickey; Matthew E. Ritchie (PLoS Comput. Biol., 2021)

Flexiplex: a versatile demultiplexer and search tool for omics data. - Oliver Cheng; Min Hao Ling; Changqing Wang; Shuyi Wu; Matthew E. Ritchie; Jonathan Göke; Noorul Amin; Nadia M. Davidson (Bioinform., 2024)