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

Autor Amarasinghe, Shanika L, Ritchie, Matthew E, Gouil, Quentin
Vydáno v Gigascience (2021)

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

Autor Silver, Jeremy D., Ritchie, Matthew E., Smyth, Gordon K.
Vydáno 2009

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

Autor Ritchie, Matthew E, Liu, Ruijie, Carvalho, Benilton S, Irizarry, Rafael A
Vydáno 2011

Illumina WG-6 BeadChip strips should be normalized separately

Autor Shi, Wei, Banerjee, Ashish, Ritchie, Matthew E, Gerondakis, Steve, Smyth, Gordon K
Vydáno 2009

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

Autor Liu, Ruijie, Dai, Zhiyin, Yeager, Meredith, Irizarry, Rafael A, Ritchie, Matthew E
Vydáno 2014

Transcriptional profiling of the epigenetic regulator Smchd1

Autor Liu, Ruijie, Chen, Kelan, Jansz, Natasha, Blewitt, Marnie E., Ritchie, Matthew E.
Vydáno v Genom Data (2015)

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

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

Using the R Package crlmm for Genotyping and Copy Number Estimation

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

BeadArray Expression Analysis Using Bioconductor

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

illuminaio: An open source IDAT parsing tool for Illumina microarrays

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

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

Autor Yin, Danqing, Ritchie, Matthew E., Jabbari, Jafar S., Beck, Tamara, Blewitt, Marnie E., Keniry, Andrew
Vydáno v Genom Data (2016)

Opportunities and challenges in long-read sequencing data analysis

Autor Amarasinghe, Shanika L., Su, Shian, Dong, Xueyi, Zappia, Luke, Ritchie, Matthew E., Gouil, Quentin
Vydáno v Genome Biol (2020)

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

Autor Su, Shian, Tian, Luyi, Dong, Xueyi, Hickey, Peter F, Freytag, Saskia, Ritchie, Matthew E
Vydáno v Bioinformatics (2020)

Statistical issues in the analysis of Illumina data

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

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

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

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

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

Easy and efficient ensemble gene set testing with EGSEA

Autor Alhamdoosh, Monther, Law, Charity W., Tian, Luyi, Sheridan, Julie M., Ng, Milica, Ritchie, Matthew E.
Vydáno v F1000Res (2017)

A guide to creating design matrices for gene expression experiments

Autor Law, Charity W., Zeglinski, Kathleen, Dong, Xueyi, Alhamdoosh, Monther, Smyth, Gordon K., Ritchie, Matthew E.
Vydáno v F1000Res (2020)

Empirical array quality weights in the analysis of microarray data

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

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

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