(Q36002387)

11 August 2017

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses (English)

1 reference

11 August 2017

0 references

1 reference

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Matthew E Ritchie

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

Marie-Liesse Asselin-Labat

10 June 2020

8

object named as

Marie-Liesse Asselin-Labat

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

author name string

Ruijie Liu

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Aliaksei Z Holik

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Shian Su

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Natasha Jansz

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Kelan Chen

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Huei San Leong

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Gordon K Smyth

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

language of work or name

English

0 references

publication date

29 April 2015

1 reference

11 August 2017

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

volume

43

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

issue

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

page(s)

e97

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

10 June 2020

copyright license

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/4551905

based on heuristic

inferred from PubMed Central ID database lookup

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

svaseq: removing batch effects and other unwanted noise from sequencing data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Normalization of RNA-seq data using factor analysis of control genes or samples

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Dissemination of scientific software with Galaxy ToolShed

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Robustly detecting differential expression in RNA sequencing data using observation weights

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Smchd1 regulates a subset of autosomal genes subject to monoallelic expression in addition to being critical for X inactivation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Epigenetic functions of smchd1 repress gene clusters on the inactive X chromosome and on autosomes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

From RNA-seq reads to differential expression results

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

ROAST: rotation gene set tests for complex microarray experiments

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Biases in Illumina transcriptome sequencing caused by random hexamer priming

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Galaxy: a web-based genome analysis tool for experimentalists

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Histone deacetylase inhibitor panobinostat induces clinical responses with associated alterations in gene expression profiles in cutaneous T-cell lymphoma

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Weighted analysis of general microarray experiments

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Empirical array quality weights in the analysis of microarray data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Galaxy: a platform for interactive large-scale genome analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Bioconductor: open software development for computational biology and bioinformatics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Epigenetic regulator Smchd1 functions as a tumor suppressor

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Control of mammary stem cell function by steroid hormone signalling.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

Weighted analysis of paired microarray experiments.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4551905

23 September 2018

Identifiers

DOI

10.1093/NAR/GKV412

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

PubMed publication ID

25925576

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25925576%20AND%20SRC:MED&resulttype=core&format=json