voom: Precision weights unlock linear model analysis tools for RNA-seq read counts (Q33741687)

29 July 2017

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

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29 July 2017

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4

Gordon K Smyth

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29 July 2017

Charity W Law

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29 July 2017

Yunshun Chen

series ordinal

2

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29 July 2017

Wei Shi

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29 July 2017

3 February 2014

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29 July 2017

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29 July 2017

15

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29 July 2017

R29

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describes a project that uses

29 July 2017

limma

object named as

limma

2 references

22 June 2022

https://europepmc.org/article/PMC/4053721

based on heuristic

inferred from PubMed Central ID database lookup

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

edgeR

object named as

edgeR package

edgeR

1 reference

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

edgeR

0 references

DESeq2

object named as

DESeq

1 reference

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

exact match

https://scigraph.springernature.com/pub.10.1186/gb-2014-15-2-r29

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cites work

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Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

21 June 2018

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

21 June 2018

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

21 June 2018

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

21 June 2018

1 reference

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

21 June 2018

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Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

21 June 2018

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Landscape of transcription in human cells

21 June 2018

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

21 June 2018

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

21 June 2018

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

21 June 2018

1 reference

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

21 June 2018

1 reference

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

21 June 2018

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

21 June 2018

1 reference

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The developmental transcriptome of Drosophila melanogaster

21 June 2018

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From RNA-seq reads to differential expression results

21 June 2018

1 reference

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Differential expression analysis for sequence count data

21 June 2018

1 reference

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

21 June 2018

1 reference

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A two-parameter generalized Poisson model to improve the analysis of RNA-seq data

21 June 2018

1 reference

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ROAST: rotation gene set tests for complex microarray experiments

21 June 2018

1 reference

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Conserved developmental transcriptomes in evolutionarily divergent species.

21 June 2018

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Understanding mechanisms underlying human gene expression variation with RNA sequencing

21 June 2018

1 reference

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

21 June 2018

1 reference

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

21 June 2018

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Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi

21 June 2018

1 reference

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RNA-Seq: a revolutionary tool for transcriptomics

21 June 2018

1 reference

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Stem cell transcriptome profiling via massive-scale mRNA sequencing

21 June 2018

1 reference

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Mapping and quantifying mammalian transcriptomes by RNA-Seq

21 June 2018

1 reference

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Moderated statistical tests for assessing differences in tag abundance

21 June 2018

1 reference

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

Using GOstats to test gene lists for GO term association

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

Empirical array quality weights in the analysis of microarray data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

X-inactivation profile reveals extensive variability in X-linked gene expression in females

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

Bioconductor: open software development for computational biology and bioinformatics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

Significance analysis of microarrays applied to the ionizing radiation response

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

The External RNA Controls Consortium: a progress report.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

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

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

A random variance model for detection of differential gene expression in small microarray experiments.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053721

30 October 2018

Identifiers

DOI

10.1186/GB-2014-15-2-R29

1 reference

Dimensions Publication ID

29 July 2017

0 references

1 reference

29 July 2017

1 reference