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
Citations
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Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics
TL;DR: It is shown that sample size, effect size, and gene abundance greatly affect the performance of all methods, and several of the methods also show non-optimal model assumptions and biased false discovery rate estimates, which can result in too large numbers of false positives.
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Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability.
Lindsay F. Rizzardi,Peter Hickey,Varenka A. Rodriguez DiBlasi,Rakel Tryggvadottir,Colin M. Callahan,Adrian Idrizi,Kasper D. Hansen,Kasper D. Hansen,Andrew P. Feinberg +8 more
TL;DR: An extensive profile of DNA methylation in neuronal and non-neuronal cells across four brain regions is reported, showing that differential epigenetic marks are enriched for DNA variants associated with neuropsychiatric traits.
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Sex-specific adipose tissue imprinting of regulatory T cells
Ajithkumar Vasanthakumar,Ajithkumar Vasanthakumar,David Chisanga,David Chisanga,Jonas Blume,Jonas Blume,Renee Gloury,Renee Gloury,Kara L. Britt,Darren C. Henstridge,Yifan Zhan,Yifan Zhan,Santiago Valle Torres,Sebastian Liene,Sebastian Liene,Nicholas Collins,Enyuan Cao,Tom Sidwell,Tom Sidwell,Chaoran Li,Raul German Spallanzani,Yang Liao,Yang Liao,Paul A. Beavis,Thomas Gebhardt,Natalie L. Trevaskis,Stephen L. Nutt,Stephen L. Nutt,Jeffrey D Zajac,Rachel A Davey,Mark A. Febbraio,Diane Mathis,Wei Shi,Wei Shi,Axel Kallies,Axel Kallies +35 more
TL;DR: It is found that sex-specific differences in T reg cells from VAT are determined by the tissue niche in a sex-hormone-dependent manner to limit adipose tissue inflammation.
Comparison of Cas9 activators in multiple species
Alejandro Chavez,Marcelle Tuttle,Benjamin W. Pruitt,Ben Ewen-Campen,Raj Chari,Dmitry Ter-Ovanesyan,Sabina J Haque,Ryan J Cecchi,Emma J. K. Kowal,Joanna Buchthal,Benjamin E. Housden,Norbert Perrimon,George M. Church,James J. Collins +13 more
TL;DR: Several groups have generated programmable transcription factors based on the versatile Cas9 protein, yet their relative potency and effectiveness across various cell types and species remain
Journal ArticleDOI
Tximeta: Reference sequence checksums for provenance identification in RNA-seq.
Michael I. Love,Charlotte Soneson,Charlotte Soneson,Peter Hickey,Peter Hickey,Lisa K. Johnson,N. T. Pierce,Lori Shepherd,Martin Morgan,Rob Patro +9 more
TL;DR: This work provides a solution in the form of an R/Bioconductor package tximeta that performs numerous annotation and metadata gathering tasks automatically on behalf of users during the import of transcript quantification files.
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