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

door Amarasinghe, Shanika L, Ritchie, Matthew E, Gouil, Quentin
Gepubliceerd in Gigascience (2021)

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

door Silver, Jeremy D., Ritchie, Matthew E., Smyth, Gordon K.
Gepubliceerd in 2009

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

door Ritchie, Matthew E, Liu, Ruijie, Carvalho, Benilton S, Irizarry, Rafael A
Gepubliceerd in 2011

Illumina WG-6 BeadChip strips should be normalized separately

door Shi, Wei, Banerjee, Ashish, Ritchie, Matthew E, Gerondakis, Steve, Smyth, Gordon K
Gepubliceerd in 2009

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

door Liu, Ruijie, Dai, Zhiyin, Yeager, Meredith, Irizarry, Rafael A, Ritchie, Matthew E
Gepubliceerd in 2014

Transcriptional profiling of the epigenetic regulator Smchd1

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

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

door Ritchie, Matthew E., Carvalho, Benilton S., Hetrick, Kurt N., Tavaré, Simon, Irizarry, Rafael A.
Gepubliceerd in 2009

Using the R Package crlmm for Genotyping and Copy Number Estimation

door Scharpf, Robert B., Irizarry, Rafael A., Ritchie, Matthew E., Carvalho, Benilton, Ruczinski, Ingo
Gepubliceerd in 2011

BeadArray Expression Analysis Using Bioconductor

door Ritchie, Matthew E., Dunning, Mark J., Smith, Mike L., Shi, Wei, Lynch, Andy G.
Gepubliceerd in 2011

illuminaio: An open source IDAT parsing tool for Illumina microarrays

door Smith, Mike L, Baggerly, Keith A., Bengtsson, Henrik, Ritchie, Matthew E., Hansen, Kasper D.
Gepubliceerd in 2013

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

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

Opportunities and challenges in long-read sequencing data analysis

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

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

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

Statistical issues in the analysis of Illumina data

door Dunning, Mark J, Barbosa-Morais, Nuno L, Lynch, Andy G, Tavaré, Simon, Ritchie, Matthew E
Gepubliceerd in 2008

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

door Dunning, Mark J, Ritchie, Matthew E, Barbosa-Morais, Nuno L, Tavaré, Simon, Lynch, Andy G
Gepubliceerd in 2008

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

door Ritchie, Matthew E, Forrest, Matthew S, Dimas, Antigone S, Daelemans, Caroline, Dermitzakis, Emmanouil T, Deloukas, Panagiotis, Tavaré, Simon
Gepubliceerd in 2010

Easy and efficient ensemble gene set testing with EGSEA

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

A guide to creating design matrices for gene expression experiments

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

Empirical array quality weights in the analysis of microarray data

door Ritchie, Matthew E, Diyagama, Dileepa, Neilson, Jody, van Laar, Ryan, Dobrovic, Alexander, Holloway, Andrew, Smyth, Gordon K
Gepubliceerd in 2006

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

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