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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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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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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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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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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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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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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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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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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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Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips

Nucleic acids research, 2010-12, Vol.38 (22), p.e204-e204

2010

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diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data

BMC bioinformatics, 2015-08, Vol.16 (1), p.258-258, Article 258

2015

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Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells

Nature immunology, 2015-06, Vol.16 (6), p.663-673

2015

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Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

Genome Biology, 2019-11, Vol.20 (1), p.236-236, Article 236

2019

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RANK ligand as a potential target for breast cancer prevention in BRCA1-mutation carriers

Nature medicine, 2016-08, Vol.22 (8), p.933-939

2016

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Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling

Nature communications, 2017-11, Vol.8 (1), p.1627-14, Article 1627

2017

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Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate

Nucleic acids research, 2021-11, Vol.49 (19), p.e109-e109

2021

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De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

Nucleic acids research, 2014-06, Vol.42 (11), p.e95-e95

2014

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ROAST: rotation gene set tests for complex microarray experiments

Bioinformatics, 2010-09, Vol.26 (17), p.2176-2182

2010

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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

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

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

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

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

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

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

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

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

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]

Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data

Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

RANK ligand as a potential target for breast cancer prevention in BRCA1-mutation carriers

Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling

Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

ROAST: rotation gene set tests for complex microarray experiments

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