Differential expression analysis of RNA-seq data at single-base resolution (Q30727551)

23 September 2017

Differential expression analysis of RNA-seq data at single-base resolution (English)

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23 September 2017

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26 June 2017

Jeffrey T Leek

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Rafael Irizarry

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4

object named as

Rafael A Irizarry

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23 September 2017

Alyssa C Frazee

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PMCID

4059460

23 September 2017

Sarven Sabunciyan

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2

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23 September 2017

6 January 2014

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23 September 2017

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23 September 2017

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23 September 2017

413-426

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23 September 2017

3

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PMCID

4059460

describes a project that uses

23 September 2017

DESeq2

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DESeq

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CZ Software Mentions: A large dataset of software mentions in the biomedical literature

edgeR

object named as

EdgeR

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CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

Differential analysis of gene regulation at transcript resolution with RNA-seq

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

Detecting differential usage of exons from RNA-seq data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

Solving the Problem: Genome Annotation Standards before the Data Deluge

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

GC-content normalization for RNA-Seq data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

The reality of pervasive transcription

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

Sequencing technology does not eliminate biological variability

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

rnaSeqMap: a Bioconductor package for RNA sequencing data exploration

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

From RNA-seq reads to differential expression results

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

Analysis and design of RNA sequencing experiments for identifying isoform regulation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

Differential expression analysis for sequence count data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

Alternative expression analysis by RNA sequencing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

TopHat: discovering splice junctions with RNA-Seq

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

Mapping and quantifying mammalian transcriptomes by RNA-Seq

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4059460

Microarrays, Empirical Bayes and the Two-Groups Model

28 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOSTATISTICS%2FKXT053

IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOSTATISTICS%2FKXT053

The case for cloud computing in genome informatics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOSTATISTICS%2FKXT053

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOSTATISTICS%2FKXT053

Identifying differentially spliced genes from two groups of RNA-seq samples

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24398039

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOSTATISTICS/KXT053

1 reference

23 September 2017

1 reference

23 September 2017

1 reference

PMCID

4059460