long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data

von Amarasinghe, Shanika L, Ritchie, Matthew E, Gouil, Quentin
Veröffentlicht in Gigascience (2021)

Microarray background correction: maximum likelihood estimation for the normal–exponential convolution

von Silver, Jeremy D., Ritchie, Matthew E., Smyth, Gordon K.
Veröffentlicht 2009

Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips

von Ritchie, Matthew E, Liu, Ruijie, Carvalho, Benilton S, Irizarry, Rafael A
Veröffentlicht 2011

Illumina WG-6 BeadChip strips should be normalized separately

von Shi, Wei, Banerjee, Ashish, Ritchie, Matthew E, Gerondakis, Steve, Smyth, Gordon K
Veröffentlicht 2009

KRLMM: an adaptive genotype calling method for common and low frequency variants

von Liu, Ruijie, Dai, Zhiyin, Yeager, Meredith, Irizarry, Rafael A, Ritchie, Matthew E
Veröffentlicht 2014

Transcriptional profiling of the epigenetic regulator Smchd1

von Liu, Ruijie, Chen, Kelan, Jansz, Natasha, Blewitt, Marnie E., Ritchie, Matthew E.
Veröffentlicht in Genom Data (2015)

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips

von Ritchie, Matthew E., Carvalho, Benilton S., Hetrick, Kurt N., Tavaré, Simon, Irizarry, Rafael A.
Veröffentlicht 2009

Using the R Package crlmm for Genotyping and Copy Number Estimation

von Scharpf, Robert B., Irizarry, Rafael A., Ritchie, Matthew E., Carvalho, Benilton, Ruczinski, Ingo
Veröffentlicht 2011

BeadArray Expression Analysis Using Bioconductor

von Ritchie, Matthew E., Dunning, Mark J., Smith, Mike L., Shi, Wei, Lynch, Andy G.
Veröffentlicht 2011

illuminaio: An open source IDAT parsing tool for Illumina microarrays

von Smith, Mike L, Baggerly, Keith A., Bengtsson, Henrik, Ritchie, Matthew E., Hansen, Kasper D.
Veröffentlicht 2013

High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS)

von Yin, Danqing, Ritchie, Matthew E., Jabbari, Jafar S., Beck, Tamara, Blewitt, Marnie E., Keniry, Andrew
Veröffentlicht in Genom Data (2016)

Opportunities and challenges in long-read sequencing data analysis

von Amarasinghe, Shanika L., Su, Shian, Dong, Xueyi, Zappia, Luke, Ritchie, Matthew E., Gouil, Quentin
Veröffentlicht in Genome Biol (2020)

CellBench: R/Bioconductor software for comparing single-cell RNA-seq analysis methods

von Su, Shian, Tian, Luyi, Dong, Xueyi, Hickey, Peter F, Freytag, Saskia, Ritchie, Matthew E
Veröffentlicht in Bioinformatics (2020)

Statistical issues in the analysis of Illumina data

von Dunning, Mark J, Barbosa-Morais, Nuno L, Lynch, Andy G, Tavaré, Simon, Ritchie, Matthew E
Veröffentlicht 2008

Spike-in validation of an Illumina-specific variance-stabilizing transformation

von Dunning, Mark J, Ritchie, Matthew E, Barbosa-Morais, Nuno L, Tavaré, Simon, Lynch, Andy G
Veröffentlicht 2008

Data analysis issues for allele-specific expression using Illumina's GoldenGate assay

von Ritchie, Matthew E, Forrest, Matthew S, Dimas, Antigone S, Daelemans, Caroline, Dermitzakis, Emmanouil T, Deloukas, Panagiotis, Tavaré, Simon
Veröffentlicht 2010

Easy and efficient ensemble gene set testing with EGSEA

von Alhamdoosh, Monther, Law, Charity W., Tian, Luyi, Sheridan, Julie M., Ng, Milica, Ritchie, Matthew E.
Veröffentlicht in F1000Res (2017)

A guide to creating design matrices for gene expression experiments

von Law, Charity W., Zeglinski, Kathleen, Dong, Xueyi, Alhamdoosh, Monther, Smyth, Gordon K., Ritchie, Matthew E.
Veröffentlicht in F1000Res (2020)

Empirical array quality weights in the analysis of microarray data

von Ritchie, Matthew E, Diyagama, Dileepa, Neilson, Jody, van Laar, Ryan, Dobrovic, Alexander, Holloway, Andrew, Smyth, Gordon K
Veröffentlicht 2006

limma powers differential expression analyses for RNA-sequencing and microarray studies

von Ritchie, Matthew E., Phipson, Belinda, Wu, Di, Hu, Yifang, Law, Charity W., Shi, Wei, Smyth, Gordon K.
Veröffentlicht in Nucleic Acids Res (2015)