Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline (Q30991698)

17 August 2017

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline (English)

1 reference

17 August 2017

1 reference

1 reference

1 reference

Frank Emmert-Streib

2

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author name string

Yasir Rahmatallah

series ordinal

1

1 reference

PMCID

4870397

17 August 2017

Galina Glazko

series ordinal

3

1 reference

17 August 2017

4 September 2015

1 reference

Briefings in Bioinformatics

17 August 2017

1 reference

17 August 2017

17

1 reference

17 August 2017

393-407

1 reference

17 August 2017

3

1 reference

PMCID

4870397

describes a project that uses

17 August 2017

DESeq2

DESeq

1 reference

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

edgeR

edgeR

1 reference

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

GSVA

GSVA

1 reference

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

limma

limma

1 reference

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

limma

0 references

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21 June 2018

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

21 June 2018

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Comparative evaluation of gene set analysis approaches for RNA-Seq data.

21 June 2018

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21 June 2018

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21 June 2018

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

21 June 2018

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Soft truncation thresholding for gene set analysis of RNA-seq data: application to a vaccine study

21 June 2018

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Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing

21 June 2018

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Gene set analysis methods: statistical models and methodological differences

21 June 2018

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Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential

21 June 2018

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GSVA: gene set variation analysis for microarray and RNA-seq data.

21 June 2018

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The limitations of simple gene set enrichment analysis assuming gene independence

21 June 2018

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Gene set analysis for self-contained tests: complex null and specific alternative hypotheses

21 June 2018

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Assessment method for a power analysis to identify differentially expressed pathways

21 June 2018

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Ten years of pathway analysis: current approaches and outstanding challenges

21 June 2018

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

21 June 2018

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

21 June 2018

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Pathway analysis of expression data: deciphering functional building blocks of complex diseases

21 June 2018

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Molecular signatures database (MSigDB) 3.0.

21 June 2018

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Linear combination test for hierarchical gene set analysis

21 June 2018

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Differential expression analysis for sequence count data

21 June 2018

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Heading down the wrong pathway: on the influence of correlation within gene sets

21 June 2018

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ROAST: rotation gene set tests for complex microarray experiments

21 June 2018

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Understanding mechanisms underlying human gene expression variation with RNA sequencing

21 June 2018

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

21 June 2018

1 reference

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

21 June 2018

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

21 June 2018

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Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

21 June 2018

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Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets

21 June 2018

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Gene set internal coherence in the context of functional profiling

21 June 2018

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Estimating accuracy of RNA-Seq and microarrays with proteomics

21 June 2018

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A general modular framework for gene set enrichment analysis

21 June 2018

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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

21 June 2018

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Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters

21 June 2018

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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

21 June 2018

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Alternative isoform regulation in human tissue transcriptomes

21 June 2018

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Gene-set analysis and reduction

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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Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4870397

Gene-set approach for expression pattern analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4870397

Comparative evaluation of gene-set analysis methods

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4870397

A multivariate extension of the gene set enrichment analysis.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4870397

Moderated statistical tests for assessing differences in tag abundance

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4870397

Improving gene set analysis of microarray data by SAM-GS.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4870397

Analyzing gene expression data in terms of gene sets: methodological issues

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4870397

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=4870397

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=4870397

Discovering statistically significant pathways in expression profiling studies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4870397

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

21 June 2018

1 reference

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A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4870397

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=4870397

Gene chips: array of hope for understanding gene regulation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4870397

Finishing bacterial genome assemblies with Mix.

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIB%2FBBV069

Multivariate Generalizations of the Wald-Wolfowitz and Smirnov Two-Sample Tests

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIB%2FBBV069

The death of microarrays?

21 January 2018

1 reference

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https://api.crossref.org/works/10.1093%2FBIB%2FBBV069

Statistical concerns about the GSEA procedure

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26342128

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIB/BBV069

1 reference

journals/bib/RahmatallahEG16

17 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

17 August 2017

1 reference

PMCID

4870397