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:Â
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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Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types.
Ying-Jiun J. Chen,Brad A. Friedman,Connie Ha,Steffen Durinck,Jinfeng Liu,John L.R. Rubenstein,Somasekar Seshagiri,Zora Modrusan +7 more
TL;DR: Single-cell RNA sequencing on the mouse embryonic medial ganglionic eminence (MGE) and on MGE-like cells differentiated from embryonic stem cells provides detailed understanding of the embryonic MGE developmental program and suggests how CINs are specified.
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Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates
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Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases
Matthew T. N. Yarnall,Eleonora I. Ioannidi,Cian Schmitt-Ulms,Rohan N. Krajeski,Justin K. Lim,Lukas Villiger,Wenyuan Zhou,Kaiyi Jiang,Sofya K. Garushyants,Nathan Roberts,Liyang Zhang,Christopher A. Vakulskas,John A. Walker,Anastasia P. Kadina,Adrianna E Zepeda,Kevin Holden,Hong-Yu Ma,Jun Xie,Guangping Gao,Lander Foquet,Greg Bial,Sara K. Donnelly,Yoshinari Miyata,Daniel R. Radiloff,Jordana M. Henderson,Andrew Ujita,Omar O. Abudayyeh,Jonathan S. Gootenberg +27 more
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Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes Is Associated With Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy
Sirisha Cheedipudi,Scot J. Matkovich,Cristian Coarfa,Xin Hu,Matthew J. Robertson,Mary E. Sweet,Matthew R.G. Taylor,Luisa Mestroni,Joseph C. Cleveland,James T. Willerson,Priyatansh Gurha,Ali J. Marian +11 more
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Environmental sensing by mature B cells is controlled by the transcription factors PU.1 and SpiB
Simon N. Willis,Julie Tellier,Julie Tellier,Yang Liao,Yang Liao,Stephanie Trezise,Stephanie Trezise,Amanda Light,Kristy O'Donnell,Kristy O'Donnell,Lee Ann Garrett-Sinha,Wei Shi,Wei Shi,David M. Tarlinton,David M. Tarlinton,David M. Tarlinton,Stephen L. Nutt,Stephen L. Nutt +17 more
TL;DR: It is shown that mice lacking both PU.1 and SpiB in mature B cells do not generate germinal centers and high-affinity antibody after protein immunization, and double-deficient B cells have a survival defect after engagement of CD40 or Toll-like receptors (TLR), despite paradoxically enhanced plasma cell differentiation.
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