voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Charity W. Law,Charity W. Law,Yunshun Chen,Yunshun Chen,Wei Shi,Wei Shi,Gordon K. Smyth,Gordon K. Smyth +7 more
TLDR
New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments, and the voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline.Abstract:
New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline. This opens access for RNA-seq analysts to a large body of methodology developed for microarrays. Simulation studies show that voom performs as well or better than count-based RNA-seq methods even when the data are generated according to the assumptions of the earlier methods. Two case studies illustrate the use of linear modeling and gene set testing methods.read more
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Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research
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TL;DR: The basic design of commonly used NGS-based methods, specifically whole exome sequencing, transcriptome, and epigenome profiling are illustrated, and recommendations for data analyses are provided.
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Understanding sequencing data as compositions: an outlook and review
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seq-ImmuCC: Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.
Ziyi Chen,Lijun Quan,Anfei Huang,Qiang Zhao,Yao Yuan,Xuye Yuan,Qin Shen,Jingzhe Shang,Yinyin Ben,F. Xiao-Feng Qin,Aiping Wu +10 more
TL;DR: A computational model named seq-ImmuCC was developed to infer the relative proportions of 10 major immune cells in mouse tissues from RNA-Seq data and generated the comprehensive landscape of immune cell compositions in 27 normal mouse tissues, which provided a comprehensive and informative measurement for the immune microenvironment inside tumor tissues.
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Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models.
TL;DR: A Poisson mixture model is proposed using a rigorous framework for parameter estimation as well as the choice of the appropriate number of clusters for clustering DGE profiles as a means to discover groups of co-expressed genes.
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Insights into beta cell regeneration for diabetes via integration of molecular landscapes in human insulinomas
Huan Wang,Huan Wang,Aaron Bender,Peng Wang,Esra Karakose,William B. Inabnet,Steven K. Libutti,Andrew Arnold,Luca Lambertini,Micheal Stang,Herbert Chen,Yumi Kasai,Milind Mahajan,Yayoi Kinoshita,Gustavo Fernandez-Ranvier,Thomas C. Becker,Karen K. Takane,Laura Walker,Shira R Saul,Rong Chen,Rong Chen,Donald K. Scott,Jorge Ferrer,Yevgeniy Antipin,Yevgeniy Antipin,Michael J. Donovan,Andrew V. Uzilov,Andrew V. Uzilov,Boris Reva,Eric E. Schadt,Eric E. Schadt,Bojan Losic,Carmen Argmann,Andrew F. Stewart +33 more
TL;DR: It is shown at the pathway level that the majority of the insulinomas display mutations, copy number variants and/or dysregulation of epigenetic modifying genes, most prominently in the polycomb and trithorax families, revealing candidates for inducing beta cell regeneration.
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