Comparison of software packages for detecting differential expression in RNA-seq studies (Q41816553)

12 October 2017

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

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12 October 2017

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3

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12 October 2017

Fatemeh Seyednasrollah

series ordinal

1

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PMCID

4293378

12 October 2017

Asta Laiho

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2

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12 October 2017

2 December 2013

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Briefings in Bioinformatics

12 October 2017

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12 October 2017

16

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12 October 2017

59-70

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12 October 2017

1

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PMCID

4293378

describes a project that uses

12 October 2017

limma

object named as

limma

Limma

2 references

22 June 2022

https://europepmc.org/article/PMC/4293378

based on heuristic

inferred from PubMed Central ID database lookup

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

DESeq2

object named as

DESeq

DESeq2

DEseq

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

DESeq2

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edgeR

object named as

edgeR

1 reference

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

cites work

Data-based filtering for replicated high-throughput transcriptome sequencing experiments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

Differential analysis of gene regulation at transcript resolution with RNA-seq

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

easyRNASeq: a bioconductor package for processing RNA-Seq data

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

RNA-Seq quantification of the human small airway epithelium transcriptome

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

Differential expression in RNA-seq: a matter of depth

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

Computational methods for transcriptome annotation and quantification using RNA-seq

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

From RNA-seq reads to differential expression results

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

Differential expression analysis for sequence count data

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

Independent filtering increases detection power for high-throughput experiments

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

Understanding mechanisms underlying human gene expression variation with RNA sequencing

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

Mapping and quantifying mammalian transcriptomes by RNA-Seq

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

Apparently low reproducibility of true differential expression discoveries in microarray studies.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4293378

18 August 2018

Identifiers

DOI

10.1093/BIB/BBT086

1 reference

journals/bib/SeyednasrollahL15

12 October 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

12 October 2017

1 reference

PMCID

4293378