Transcriptional profiling of the epigenetic regulator Smchd1

by Ruijie Liu, Kelan Chen, Natasha Jansz, Marnie E. Blewitt, Matthew E. Ritchie
Published 2016-03-01

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR [version 2; referees: 3 approved]

by Charity W. Law, Monther Alhamdoosh, Shian Su, Gordon K. Smyth, Matthew E. Ritchie
Published 2016-11-01

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR [version 1; referees: 3 approved]

by Charity W. Law, Monther Alhamdoosh, Shian Su, Gordon K. Smyth, Matthew E. Ritchie
Published 2016-06-01

Using the R Package crlmm for Genotyping and Copy Number Estimation

by Robert B. Scharpf, Rafael A. Irizarry, Matthew E. Ritchie, Benilton Carvalho, Ingo Ruczinski
Published 2011-05-01

Opportunities and challenges in long-read sequencing data analysis

by Shanika L. Amarasinghe, Shian Su, Xueyi Dong, Luke Zappia, Matthew E. Ritchie, Quentin Gouil
Published 2020-02-01

illuminaio: An open source IDAT parsing tool for Illumina microarrays [v1; ref status: indexed, http://f1000r.es/2f5]

by Mike L Smith, Keith A. Baggerly, Henrik Bengtsson, Matthew E. Ritchie, Kasper D. Hansen
Published 2013-12-01

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

by Danqing Yin, Matthew E. Ritchie, Jafar S. Jabbari, Tamara Beck, Marnie E. Blewitt, Andrew Keniry
Published 2016-12-01

BeadArray expression analysis using bioconductor.

by Matthew E Ritchie, Mark J Dunning, Mike L Smith, Wei Shi, Andy G Lynch
Published 2011-12-01

A guide to creating design matrices for gene expression experiments [version 1; peer review: 2 approved]

by Charity W. Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, Gordon K. Smyth, Matthew E. Ritchie
Published 2020-12-01

Easy and efficient ensemble gene set testing with EGSEA [version 1; referees: 1 approved, 3 approved with reservations]

by Monther Alhamdoosh, Charity W. Law, Luyi Tian, Julie M. Sheridan, Milica Ng, Matthew E. Ritchie
Published 2017-11-01

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR [version 3; referees: 3 approved]

by Charity W. Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi Tian, Gordon K. Smyth, Matthew E. Ritchie
Published 2018-12-01

Transcriptome and H3K27 tri-methylation profiling of Ezh2-deficient lung epithelium

by Aliaksei Z. Holik, Laura A. Galvis, Aaron T.L. Lun, Matthew E. Ritchie, Marie-Liesse Asselin-Labat
Published 2015-09-01

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.

by Luyi Tian, Shian Su, Xueyi Dong, Daniela Amann-Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J Hilton, Shalin H Naik, Matthew E Ritchie
Published 2018-08-01

shRNA-seq data analysis with edgeR [v1; ref status: indexed, http://f1000r.es/38s]

by Zhiyin Dai, Julie M. Sheridan, Linden J. Gearing, Darcy L. Moore, Shian Su, Ross A. Dickins, Marnie E. Blewitt, Matthew E. Ritchie
Published 2014-04-01

Modifier effects between regulatory and protein-coding variation.

by Antigone S Dimas, Barbara E Stranger, Claude Beazley, Robert D Finn, Catherine E Ingle, Matthew S Forrest, Matthew E Ritchie, Panos Deloukas, Simon Tavaré, Emmanouil T Dermitzakis
Published 2008-10-01

edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens [v2; ref status: indexed, http://f1000r.es/4kw]

by Zhiyin Dai, Julie M. Sheridan, Linden J. Gearing, Darcy L. Moore, Shian Su, Sam Wormald, Stephen Wilcox, Liam O'Connor, Ross A. Dickins, Marnie E. Blewitt, Matthew E. Ritchie
Published 2014-10-01

Thymospheres Are Formed by Mesenchymal Cells with the Potential to Generate Adipocytes, but Not Epithelial Cells

by Julie M. Sheridan, Ashleigh Keown, Antonia Policheni, Siti N.A. Roesley, Noa Rivlin, Noam Kadouri, Matthew E. Ritchie, Reema Jain, Jakub Abramson, Tracy S.P. Heng, Daniel H.D. Gray
Published 2017-10-01

Gene network disruptions and neurogenesis defects in the adult Ts1Cje mouse model of Down syndrome.

by Chelsee A Hewitt, King-Hwa Ling, Tobias D Merson, Ken M Simpson, Matthew E Ritchie, Sarah L King, Melanie A Pritchard, Gordon K Smyth, Tim Thomas, Hamish S Scott, Anne K Voss
Published 2010-07-01

Global Changes in the Mammary Epigenome Are Induced by Hormonal Cues and Coordinated by Ezh2

by Bhupinder Pal, Toula Bouras, Wei Shi, François Vaillant, Julie M. Sheridan, Naiyang Fu, Kelsey Breslin, Kun Jiang, Matthew E. Ritchie, Matthew Young, Geoffrey J. Lindeman, Gordon K. Smyth, Jane E. Visvader
Published 2013-02-01

Deciphering the Innate Lymphoid Cell Transcriptional Program

by Cyril Seillet, Lisa A. Mielke, Daniela B. Amann-Zalcenstein, Shian Su, Jerry Gao, Francisca F. Almeida, Wei Shi, Matthew E. Ritchie, Shalin H. Naik, Nicholas D. Huntington, Sebastian Carotta, Gabrielle T. Belz
Published 2016-10-01