Yunshun Chen
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Voom: precision weights unlock linear model analysis tools for RNA-seq read counts
CW Law, Y Chen, W Shi, GK Smyth
Genome Biology 15 (2), R29, 2014
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
DJ McCarthy, Y Chen, GK Smyth
Nucleic acids research 40 (10), 4288-4297, 2012
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
S Anders, DJ McCarthy, Y Chen, M Okoniewski, GK Smyth, W Huber, ...
Nature protocols 8 (9), 1765-1786, 2013
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
Y Chen, ATL Lun, GK Smyth
F1000Research 5, 2016
It’s DE-licious: a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR
ATL Lun, Y Chen, GK Smyth
Statistical Genomics, 391-416, 2016
Differential Expression Analysis of Complex RNA-seq Experiments Using edgeR
Y Chen, ATL Lun, GK Smyth
Statistical Analysis of Next Generation Sequencing Data, 51-74, 2014
Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling
B Pal, Y Chen, F Vaillant, P Jamieson, L Gordon, AC Rios, S Wilcox, N Fu, ...
Nature communications 8 (1), 1-14, 2017
edgeR: differential expression analysis of digital gene expression data User’s Guide
Y Chen, D McCarthy, M Robinson, GK Smyth
Bioconductor User’s Guide, 2014
statmod: Statistical modeling
G Smyth, Y Hu, P Dunn, B Phipson, Y Chen
R package version 1 (4), 17, 2013
Intraclonal plasticity in mammary tumors revealed through large-scale single-cell resolution 3d imaging
AC Rios, BD Capaldo, F Vaillant, B Pal, R van Ineveld, CA Dawson, ...
Cancer cell 35 (4), 618-632. e6, 2019
Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer
D Merino, TS Weber, A Serrano, F Vaillant, K Liu, B Pal, L Di Stefano, ...
Nature communications 10 (1), 1-12, 2019
Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
Y Chen, B Pal, JE Visvader, GK Smyth
F1000Research 6, 2017
c-Myb Regulates the T-Bet-Dependent Differentiation Program in B Cells to Coordinate Antibody Responses
D Piovesan, J Tempany, A Di Pietro, I Baas, C Yiannis, K O’Donnell, ...
Cell Reports 19 (3), 461-470, 2017
Regulation of germinal center responses and B-cell memory by the chromatin modifier MOZ
KL Good-Jacobson, Y Chen, AK Voss, GK Smyth, T Thomas, D Tarlinton
Proceedings of the National Academy of Sciences 111 (26), 9585-9590, 2014
Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway
CE Weeden, Y Chen, SB Ma, Y Hu, G Ramm, KD Sutherland, GK Smyth, ...
PLOS Biology 15 (1), e2000731, 2017
A single‐cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast
B Pal, Y Chen, F Vaillant, BD Capaldo, R Joyce, X Song, VL Bryant, ...
The EMBO journal 40 (11), e107333, 2021
Integration of microRNA signatures of distinct mammary epithelial cell types with their gene expression and epigenetic portraits
B Pal, Y Chen, A Bert, Y Hu, JM Sheridan, T Beck, W Shi, K Satterley, ...
Breast Cancer Research 17 (1), 1-16, 2015
Mutant TRP53 exerts a target gene-selective dominant-negative effect to drive tumor development
BJ Aubrey, A Janic, Y Chen, C Chang, EC Lieschke, ST Diepstraten, ...
Genes & development 32 (21-22), 1420-1429, 2018
Foxp1 is indispensable for ductal morphogenesis and controls the exit of mammary stem cells from quiescence
NY Fu, B Pal, Y Chen, FC Jackling, M Milevskiy, F Vaillant, BD Capaldo, ...
Developmental cell 47 (5), 629-644. e8, 2018
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline [version 2; referees: 5 approved …
Y Chen, AT Lun, GK Smyth
PubMed Abstract| Publisher Full Text| Free Full Text, 0
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