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

Por Amarasinghe, Shanika L, Ritchie, Matthew E, Gouil, Quentin
Publicado no Gigascience (2021)

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

Por Silver, Jeremy D., Ritchie, Matthew E., Smyth, Gordon K.
Publicado em 2009

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

Por Ritchie, Matthew E, Liu, Ruijie, Carvalho, Benilton S, Irizarry, Rafael A
Publicado em 2011

Illumina WG-6 BeadChip strips should be normalized separately

Por Shi, Wei, Banerjee, Ashish, Ritchie, Matthew E, Gerondakis, Steve, Smyth, Gordon K
Publicado em 2009

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

Por Liu, Ruijie, Dai, Zhiyin, Yeager, Meredith, Irizarry, Rafael A, Ritchie, Matthew E
Publicado em 2014

Transcriptional profiling of the epigenetic regulator Smchd1

Por Liu, Ruijie, Chen, Kelan, Jansz, Natasha, Blewitt, Marnie E., Ritchie, Matthew E.
Publicado no Genom Data (2015)

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

Por Ritchie, Matthew E., Carvalho, Benilton S., Hetrick, Kurt N., Tavaré, Simon, Irizarry, Rafael A.
Publicado em 2009

Using the R Package crlmm for Genotyping and Copy Number Estimation

Por Scharpf, Robert B., Irizarry, Rafael A., Ritchie, Matthew E., Carvalho, Benilton, Ruczinski, Ingo
Publicado em 2011

BeadArray Expression Analysis Using Bioconductor

Por Ritchie, Matthew E., Dunning, Mark J., Smith, Mike L., Shi, Wei, Lynch, Andy G.
Publicado em 2011

illuminaio: An open source IDAT parsing tool for Illumina microarrays

Por Smith, Mike L, Baggerly, Keith A., Bengtsson, Henrik, Ritchie, Matthew E., Hansen, Kasper D.
Publicado em 2013

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

Por Yin, Danqing, Ritchie, Matthew E., Jabbari, Jafar S., Beck, Tamara, Blewitt, Marnie E., Keniry, Andrew
Publicado no Genom Data (2016)

Opportunities and challenges in long-read sequencing data analysis

Por Amarasinghe, Shanika L., Su, Shian, Dong, Xueyi, Zappia, Luke, Ritchie, Matthew E., Gouil, Quentin
Publicado no Genome Biol (2020)

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

Por Su, Shian, Tian, Luyi, Dong, Xueyi, Hickey, Peter F, Freytag, Saskia, Ritchie, Matthew E
Publicado no Bioinformatics (2020)

Statistical issues in the analysis of Illumina data

Por Dunning, Mark J, Barbosa-Morais, Nuno L, Lynch, Andy G, Tavaré, Simon, Ritchie, Matthew E
Publicado em 2008

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

Por Dunning, Mark J, Ritchie, Matthew E, Barbosa-Morais, Nuno L, Tavaré, Simon, Lynch, Andy G
Publicado em 2008

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

Por Ritchie, Matthew E, Forrest, Matthew S, Dimas, Antigone S, Daelemans, Caroline, Dermitzakis, Emmanouil T, Deloukas, Panagiotis, Tavaré, Simon
Publicado em 2010

Easy and efficient ensemble gene set testing with EGSEA

Por Alhamdoosh, Monther, Law, Charity W., Tian, Luyi, Sheridan, Julie M., Ng, Milica, Ritchie, Matthew E.
Publicado no F1000Res (2017)

A guide to creating design matrices for gene expression experiments

Por Law, Charity W., Zeglinski, Kathleen, Dong, Xueyi, Alhamdoosh, Monther, Smyth, Gordon K., Ritchie, Matthew E.
Publicado no F1000Res (2020)

Empirical array quality weights in the analysis of microarray data

Por Ritchie, Matthew E, Diyagama, Dileepa, Neilson, Jody, van Laar, Ryan, Dobrovic, Alexander, Holloway, Andrew, Smyth, Gordon K
Publicado em 2006

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

Por Ritchie, Matthew E., Phipson, Belinda, Wu, Di, Hu, Yifang, Law, Charity W., Shi, Wei, Smyth, Gordon K.
Publicado no Nucleic Acids Res (2015)