RNA-Seq differential expression analysis: An extended review and a software tool
Published 2017 View Full Article
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Title
RNA-Seq differential expression analysis: An extended review and a software tool
Authors
Keywords
Gene expression, Software tools, RNA analysis, RNA sequencing, Genome analysis, Human genomics, Genome annotation, Transcriptome analysis
Journal
PLoS One
Volume 12, Issue 12, Pages e0190152
Publisher
Public Library of Science (PLoS)
Online
2017-12-22
DOI
10.1371/journal.pone.0190152
References
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- The devil in the details of RNA-seq
- (2014) Anton Kratz et al. NATURE BIOTECHNOLOGY
- A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data
- (2014) Zong Hong Zhang et al. PLoS One
- EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments
- (2013) Ning Leng et al. BIOINFORMATICS
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- Comparison of software packages for detecting differential expression in RNA-seq studies
- (2013) F. Seyednasrollah et al. BRIEFINGS IN BIOINFORMATICS
- Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
- (2013) Franck Rapaport et al. GENOME BIOLOGY
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- STAR: ultrafast universal RNA-seq aligner
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- Assessing the gain of biological data integration in gene networks inference
- (2012) Fábio FR Vicente et al. BMC GENOMICS
- GENCODE: The reference human genome annotation for The ENCODE Project
- (2012) J. Harrow et al. GENOME RESEARCH
- Differential analysis of gene regulation at transcript resolution with RNA-seq
- (2012) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- Wisdom of crowds for robust gene network inference
- (2012) Daniel Marbach et al. NATURE METHODS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Differential expression in RNA-seq: A matter of depth
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- (2011) Manuel Garber et al. NATURE METHODS
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- Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
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- (2009) H. Li et al. BIOINFORMATICS
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
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- RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
- (2008) J. C. Marioni et al. GENOME RESEARCH
- Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
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- (2008) Zhong Wang et al. NATURE REVIEWS GENETICS
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