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The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

Nucleic acids research, 2019-05, Vol.47 (8), p.e47-e47

2019

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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

Bioinformatics, 2014-04, Vol.30 (7), p.923-930

2014

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The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

Nucleic acids research, 2013-05, Vol.41 (10), p.e108-e108

2013

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Camera: a competitive gene set test accounting for inter-gene correlation

Nucleic acids research, 2012-09, Vol.40 (17), p.e133-e133

2012

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Herschel Detects a Massive Dust Reservoir in Supernova 1987A

Science (American Association for the Advancement of Science), 2011-09, Vol.333 (6047), p.1258-1261

2011

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Common-Resolution Convolution Kernels for Space- and Ground-Based Telescopes

Publications of the Astronomical Society of the Pacific, 2011-10, Vol.123 (908), p.1218-1236

2011

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ELDA: Extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays

Journal of immunological methods, 2009-08, Vol.347 (1), p.70-78

2009

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csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

Nucleic acids research, 2016-03, Vol.44 (5), p.e45-e45

2016

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Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

Nucleic acids research, 2012-05, Vol.40 (10), p.4288-4297

2012

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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Bioinformatics, 2010-01, Vol.26 (1), p.139-140

2010

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Gene ontology analysis for RNA-seq: accounting for selection bias

Genome biology, 2010-02, Vol.11 (2), p.R14-R14, Article R14

2010

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limma powers differential expression analyses for RNA-sequencing and microarray studies

Nucleic acids research, 2015-04, Vol.43 (7), p.e47-e47

2015

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ROBUST HYPERPARAMETER ESTIMATION PROTECTS AGAINST HYPERVARIABLE GENES AND IMPROVES POWER TO DETECT DIFFERENTIAL EXPRESSION

The annals of applied statistics, 2016-06, Vol.10 (2), p.946-963

2016

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voom: precision weights unlock linear model analysis tools for RNA-seq read counts

Genome biology, 2014-02, Vol.15 (2), p.R29-R29, Article R29

2014

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Testing significance relative to a fold-change threshold is a TREAT

Bioinformatics, 2009-03, Vol.25 (6), p.765-771

2009

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Moderated statistical tests for assessing differences in tag abundance

Bioinformatics, 2007-11, Vol.23 (21), p.2881-2887

2007

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Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

Nature protocols, 2013-09, Vol.8 (9), p.1765-1786

2013

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Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

Statistical Applications in Genetics and Molecular Biology, 2004-02, Vol.3 (1), p.3-25

Smyth, Gordon K

2004

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A single‐cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast

The EMBO journal, 2021-06, Vol.40 (11), p.e107333-n/a

2021

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Corneal dystrophies

Orphanet journal of rare diseases, 2009-02, Vol.4 (1), p.7-7, Article 7

Klintworth, Gordon K

2009

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Blimp-1 controls plasma cell function through the regulation of immunoglobulin secretion and the unfolded protein response

Nature immunology, 2016-03, Vol.17 (3), p.323-330

2016

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It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR

Methods in molecular biology (Clifton, N.J.), 2016, Vol.1418, p.391

2016

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Neither random nor censored: estimating intensity-dependent probabilities for missing values in label-free proteomics

Bioinformatics (Oxford, England), 2023-05, Vol.39 (5)

2023

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Determinants of Insecticide Resistance Evolution: Comparative Analysis Among Heliothines

Annual review of entomology, 2022-01, Vol.67 (1), p.387-406

2022

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From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline [version 2; peer review: 5 approved]

F1000 research, 2016, Vol.5, p.1438-1438

2016

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The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

Camera: a competitive gene set test accounting for inter-gene correlation

Herschel Detects a Massive Dust Reservoir in Supernova 1987A

Common-Resolution Convolution Kernels for Space- and Ground-Based Telescopes

ELDA: Extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Gene ontology analysis for RNA-seq: accounting for selection bias

limma powers differential expression analyses for RNA-sequencing and microarray studies

ROBUST HYPERPARAMETER ESTIMATION PROTECTS AGAINST HYPERVARIABLE GENES AND IMPROVES POWER TO DETECT DIFFERENTIAL EXPRESSION

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

Testing significance relative to a fold-change threshold is a TREAT

Moderated statistical tests for assessing differences in tag abundance

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

A single‐cell RNA expression atlas of normal, preneoplastic and tumorigenic states in the human breast

Corneal dystrophies

Blimp-1 controls plasma cell function through the regulation of immunoglobulin secretion and the unfolded protein response

It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR

Neither random nor censored: estimating intensity-dependent probabilities for missing values in label-free proteomics

Determinants of Insecticide Resistance Evolution: Comparative Analysis Among Heliothines

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline [version 2; peer review: 5 approved]

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