How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? (Q38889056)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

title

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference

1 reference

corrigendum / erratum

Erratum: How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Marek Gierliński

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Alexander Sherstnev

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Vijender Singh

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Nicola Wrobel

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

language of work or name

English

0 references

publication date

28 March 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

volume

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

issue

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

page(s)

839-851

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

31 March 2020

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/4878611

based on heuristic

inferred from PubMed Central ID database lookup

cites work

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Systematic integration of RNA-Seq statistical algorithms for accurate detection of differential gene expression patterns

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Error estimates for the analysis of differential expression from RNA-seq count data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

HTSeq--a Python framework to work with high-throughput sequencing data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

compcodeR--an R package for benchmarking differential expression methods for RNA-seq data.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Evaluation of read count based RNAseq analysis methods

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

RNA-seq differential expression studies: more sequence or more replication?

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Revisiting global gene expression analysis

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Normalization, testing, and false discovery rate estimation for RNA-sequencing data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Differential expression in RNA-seq: a matter of depth

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Snf2-family proteins: chromatin remodellers for any occasion

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Synthetic spike-in standards for RNA-seq experiments

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Differential expression analysis for sequence count data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Polymorphic Cis- and Trans-Regulation of Human Gene Expression

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Statistical design and analysis of RNA sequencing data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Understanding mechanisms underlying human gene expression variation with RNA sequencing

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Transcriptome genetics using second generation sequencing in a Caucasian population

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

A benchmark for statistical microarray data analysis that preserves actual biological and technical variance

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

How to map billions of short reads onto genomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

TopHat: discovering splice junctions with RNA-Seq

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Alternative isoform regulation in human tissue transcriptomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

A haplotype map of the human genome

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Fundamentals of experimental design for cDNA microarrays

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

ATP-dependent nucleosome remodeling

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Dissecting the regulatory circuitry of a eukaryotic genome

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Five SWI genes are required for expression of the HO gene in yeast

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Genes affecting the regulation of SUC2 gene expression by glucose repression in Saccharomyces cerevisiae

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Preparation of high molecular weight RNA

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Improved statistical tests for differential gene expression by shrinking variance components estimates.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Comparison of software packages for detecting differential expression in RNA-seq studies

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Sequencing technology does not eliminate biological variability

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

A functional interaction between the C-terminal domain of RNA polymerase II and the negative regulator SIN1.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Pvclust: an R package for assessing the uncertainty in hierarchical clustering.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4878611

Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities

22 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27022035

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Collective judgment predicts disease-associated single nucleotide variants

1 reference

2 April 2022

https://opencitations.net/index/coci/api/v1/references/10.1261/RNA.053959.115

On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other

1 reference

2 April 2022

https://opencitations.net/index/coci/api/v1/references/10.1261/RNA.053959.115

Identifiers

DOI

10.1261/RNA.053959.115

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

PubMed publication ID

27022035

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27022035%20AND%20SRC:MED&resulttype=core&format=json