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 (Q36368819)

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English	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	scientific article

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scholarly article

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Europe PubMed Central

13 August 2017

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 (English)

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Europe PubMed Central

13 August 2017

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Saccharomyces cerevisiae

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7

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Europe PubMed Central

13 August 2017

Natapol Pornputtapong

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Natapol Pornputtapong

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Linn Fagerberg

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Intawat Nookaew

1

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Intawat Nookaew

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Europe PubMed Central

13 August 2017

2

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Marta Papini

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Europe PubMed Central

13 August 2017

Gionata Scalcinati

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Gionata Scalcinati

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Europe PubMed Central

13 August 2017

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Matthias Uhlén

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Europe PubMed Central

13 August 2017

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publication date

10 September 2012

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Europe PubMed Central

13 August 2017

Nucleic Acids Research

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Europe PubMed Central

13 August 2017

40

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Europe PubMed Central

13 August 2017

10084-10097

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Europe PubMed Central

13 August 2017

20

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Europe PubMed Central

13 August 2017

copyright license

Creative Commons Attribution-NonCommercial 3.0 Unported

7 November 2016

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April 2022 Public Data File from Crossref

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Europe PubMed Central

22 June 2022

https://europepmc.org/article/PMC/3488244

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Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

1 reference

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30 September 2017

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

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Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis

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30 September 2017

Differential expression in RNA-seq: a matter of depth

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A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

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30 September 2017

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

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30 September 2017

Microarrays, deep sequencing and the true measure of the transcriptome

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30 September 2017

Computational methods for transcriptome annotation and quantification using RNA-seq

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Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

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Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads

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30 September 2017

Differential expression analysis for sequence count data

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30 September 2017

De novo assembly and analysis of RNA-seq data.

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30 September 2017

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

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Comprehensive comparative analysis of strand-specific RNA sequencing methods

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30 September 2017

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

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30 September 2017

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

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30 September 2017

Comprehensive survey of SNPs in the Affymetrix exon array using the 1000 Genomes dataset

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

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Fast and SNP-tolerant detection of complex variants and splicing in short reads

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30 September 2017

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30 September 2017

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Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

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Europe PubMed Central

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