Count-based differential expression analysis of RNA sequencing data using R and Bioconductor (Q29577114)

Simon Anders

1

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Mark D. Robinson

Mark D Robinson

7

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Wolfgang Huber

Wolfgang Huber

6

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Gordon K Smyth

5

Gordon K Smyth

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author name string

Yunshun Chen

3

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Michal Okoniewski

4

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language of work or name

English

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publication date

September 2013

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published in

Nature Protocols

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volume

8

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issue

9

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page(s)

1765-86

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uses

Bioconductor

1 reference

https://www.ncbi.nlm.nih.gov/pubmed/23975260

Mapping and quantifying mammalian transcriptomes by RNA-Seq

26 April 2017

cites work

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

RNA-Seq: a revolutionary tool for transcriptomics

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Differential expression analysis for sequence count data

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

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

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Bioconductor: open software development for computational biology and bioinformatics

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Proteomic analysis reveals new cardiac-specific dystrophin-associated proteins

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Full-length transcriptome assembly from RNA-Seq data without a reference genome

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

TopHat: discovering splice junctions with RNA-Seq

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Capturing heterogeneity in gene expression studies by surrogate variable analysis

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

How to map billions of short reads onto genomes

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

The Sequence Alignment/Map format and SAMtools

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

A scaling normalization method for differential expression analysis of RNA-seq data

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

STAR: ultrafast universal RNA-seq aligner

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Tackling the widespread and critical impact of batch effects in high-throughput data

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Moderated statistical tests for assessing differences in tag abundance

26 April 2017

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Small-sample estimation of negative binomial dispersion, with applications to SAGE data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Copy-number-aware differential analysis of quantitative DNA sequencing data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Epigenetic expansion of VHL-HIF signal output drives multiorgan metastasis in renal cancer.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Tools for mapping high-throughput sequencing data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

baySeq: empirical Bayesian methods for identifying differential expression in sequence count data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

A powerful and flexible approach to the analysis of RNA sequence count data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Differential expression in RNA-seq: a matter of depth

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

A comparison of methods for differential expression analysis of RNA-seq data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Detecting differential usage of exons from RNA-seq data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Identifying differentially expressed transcripts from RNA-seq data with biological variation

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Sex-specific and lineage-specific alternative splicing in primates

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Sequencing technology does not eliminate biological variability

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Statistical design and analysis of RNA sequencing data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Using control genes to correct for unwanted variation in microarray data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Reproducible research: a bioinformatics case study

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Fast and SNP-tolerant detection of complex variants and splicing in short reads

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Savant: genome browser for high-throughput sequencing data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Human immunodeficiency virus-1 Tat activates NF-κB via physical interaction with IκB-α and p65.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Conservation of an RNA regulatory map between Drosophila and mammals

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Independent filtering increases detection power for high-throughput experiments

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Removing technical variability in RNA-seq data using conditional quantile normalization

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

GC-content normalization for RNA-Seq data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

easyRNASeq: a bioconductor package for processing RNA-Seq data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.099

Savant Genome Browser 2: visualization and analysis for population-scale genomics

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23975260

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NPROT.2013.099

1 reference

Consolidated OpenCitations Corpus – April 2017

Dimensions Publication ID

1 reference

1033430059

0 references

358444

1 reference

Consolidated OpenCitations Corpus – April 2017

358444

PubMed publication ID

23975260

1 reference

Consolidated OpenCitations Corpus – April 2017