limma powers differential expression analyses for RNA-sequencing and microarray studies (Q29617988)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25605792

30 April 2017

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Belinda Phipson

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Gordon K Smyth

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

author name string

Di Wu

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Yifang Hu

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Charity W Law

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Wei Shi

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25605792

31 May 2020

language of work or name

1 reference

30 April 2017

publication date

20 April 2015

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25605792

30 April 2017

published in

Nucleic Acids Research

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25605792

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

volume

43

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25605792

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

issue

7

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25605792

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

page(s)

e47

2 references

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30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

31 May 2020

copyright license

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Direct generation of functional dopaminergic neurons from mouse and human fibroblasts

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Understanding mechanisms underlying human gene expression variation with RNA sequencing

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

MAGMA: analysis of two-channel microarrays made easy

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

WebArray: an online platform for microarray data analysis

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

RACE: Remote Analysis Computation for gene Expression data

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Bioconductor: open software development for computational biology and bioinformatics

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Normalization of cDNA microarray data

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Gene ontology: tool for the unification of biology

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Statistical methods for assessing agreement between two methods of clinical measurement

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Pax5 loss imposes a reversible differentiation block in B-progenitor acute lymphoblastic leukemia

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Guide: a desktop application for analysing gene expression data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Gene-expression data integration to squamous cell lung cancer subtypes reveals drug sensitivity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Separate-channel analysis of two-channel microarrays: recovering inter-spot information

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Molecular signatures database (MSigDB) 3.0.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

RPPanalyzer: Analysis of reverse-phase protein array data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

ROAST: rotation gene set tests for complex microarray experiments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Transcriptome analyses of mouse and human mammary cell subpopulations reveal multiple conserved genes and pathways

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Estimating the proportion of microarray probes expressed in an RNA sample

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Aire-deficient C57BL/6 mice mimicking the common human 13-base pair deletion mutation present with only a mild autoimmune phenotype

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Microarray background correction: maximum likelihood estimation for the normal-exponential convolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

NuGO contributions to GenePattern.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Integrative analysis of RUNX1 downstream pathways and target genes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

A comparison of background correction methods for two-colour microarrays

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Goulphar: rapid access and expertise for standard two-color microarray normalization methods

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Empirical array quality weights in the analysis of microarray data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Reproducible research: a bioinformatics case study

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

affylmGUI: a graphical user interface for linear modeling of single channel microarray data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

limmaGUI: a graphical user interface for linear modeling of microarray data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Changes in gene expression profiles in developing B cells of murine bone marrow

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

A whole genome scan for quantitative trait loci affecting milk protein percentage in Israeli-Holstein cattle, by means of selective milk DNA pooling in a daughter design, using an adjusted false discovery rate criterion.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Control of mammary stem cell function by steroid hormone signalling.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Use of within-array replicate spots for assessing differential expression in microarray experiments

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402510

Improved background correction for spotted DNA microarrays

26 November 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/25605792

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

3 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25605792

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25605792

3 references

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25605792

31 May 2020

PubMed publication ID

3 references

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25605792%20AND%20SRC:MED&resulttype=core&format=json