Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
TLDR
This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.Abstract:
In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
.read more
Citations
More filters
Journal ArticleDOI
HTSeq—a Python framework to work with high-throughput sequencing data
TL;DR: This work presents HTSeq, a Python library to facilitate the rapid development of custom scripts for high-throughput sequencing data analysis, and presents htseq-count, a tool developed with HTSequ that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.
Journal ArticleDOI
Comprehensive Integration of Single-Cell Data.
Tim Stuart,Andrew Butler,Paul J. Hoffman,Christoph Hafemeister,Efthymia Papalexi,William M. Mauck,Yuhan Hao,Marlon Stoeckius,Peter Smibert,Rahul Satija +9 more
TL;DR: A strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities.
Journal ArticleDOI
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
TL;DR: This protocol describes all the steps necessary to process a large set of raw sequencing reads and create lists of gene transcripts, expression levels, and differentially expressed genes and transcripts.
Journal ArticleDOI
Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19.
Daniel Blanco-Melo,Benjamin E. Nilsson-Payant,Wen-Chun Liu,Skyler Uhl,Daisy A. Hoagland,Rasmus Møller,Tristan X. Jordan,Kohei Oishi,Maryline Panis,David H. Sachs,Taia T. Wang,Robert E. Schwartz,Jean K. Lim,Randy A. Albrecht,Benjamin R. tenOever +14 more
TL;DR: It is proposed that reduced innate antiviral defenses coupled with exuberant inflammatory cytokine production are the defining and driving features of COVID-19.
Journal ArticleDOI
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
Enis Afgan,Dannon Baker,Bérénice Batut,Marius van den Beek,Dave Bouvier,Martin Čech,John Chilton,Dave Clements,Nate Coraor,Björn Grüning,Aysam Guerler,Jennifer Hillman-Jackson,Saskia Hiltemann,Vahid Jalili,Helena Rasche,Nicola Soranzo,Jeremy Goecks,James Taylor,Anton Nekrutenko,Daniel Blankenberg +19 more
TL;DR: Improvements to Galaxy's core framework, user interface, tools, and training materials enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed.
References
More filters
Journal ArticleDOI
The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq
TL;DR: This paper proposed a new statistical test for assessing differential gene expression using RNA sequencing (RNA-Seq) data, which is based on the NBP parameterization of the negative binomial distribution.
Journal ArticleDOI
The pea aphid genome sequence brings theories of insect defense into question
TL;DR: The genome sequence of the pea aphid is the first for a basal hemimetabolous insect and provides insights into developmental plasticity, symbiosis and insect immunity.
Journal ArticleDOI
ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets
TL;DR: ReCount is an online resource of RNA-seq gene count tables and auxilliary data built from raw RNA sequencing data from 18 different published studies comprising 475 samples and over 8 billion reads, allowing statistical and computational scientists to consider alternative parameter values.
Posted Content
Near-optimal RNA-Seq quantification
TL;DR: Software implementing the approach, called kallisto, can be used to analyze 30 million unaligned paired-end RNA-Seq reads in less than 5 minutes on a standard laptop computer while providing results as accurate as those of the best existing tools.
Journal ArticleDOI
Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages
TL;DR: In this article, the absence of transcription initiation regulation for RNA polymerase II in the protozoan parasite Trypanosoma brucei greatly simplifies the task of elucidating the contribution of translation to global gene expression.