Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis (Q30853974)

27 June 2017

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title

Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis (English)

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27 June 2017

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Francesca Finotello

1

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author name string

Barbara Di Camillo

series ordinal

2

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27 June 2017

publication date

18 September 2014

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Briefings in functional genomics

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published in

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volume

14

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27 June 2017

issue

2

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27 June 2017

page(s)

130-142

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describes a project that uses

27 June 2017

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The transcriptional landscape of the yeast genome defined by RNA sequencing

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Next-generation DNA sequencing

21 January 2018

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RNA-Seq: a revolutionary tool for transcriptomics

21 January 2018

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A comparison of analog and Next-Generation transcriptomic tools for mammalian studies.

21 January 2018

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The beginning of the end for microarrays?

21 January 2018

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RNA-Seq: revelation of the messengers

21 January 2018

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Stem cell transcriptome profiling via massive-scale mRNA sequencing

21 January 2018

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Mapping and quantifying mammalian transcriptomes by RNA-Seq

21 January 2018

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

21 January 2018

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De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology

21 January 2018

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Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing.

21 January 2018

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Identification of novel transcripts in annotated genomes using RNA-Seq

21 January 2018

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Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

21 January 2018

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Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

21 January 2018

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From RNA-seq reads to differential expression results

21 January 2018

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Genomics: the state of the art in RNA-seq analysis.

21 January 2018

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Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

21 January 2018

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Biases in Illumina transcriptome sequencing caused by random hexamer priming

21 January 2018

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Modelling and simulating generic RNA-Seq experiments with the flux simulator

21 January 2018

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Benchmarking short sequence mapping tools

21 January 2018

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Systematic evaluation of spliced alignment programs for RNA-seq data

21 January 2018

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Sense from sequence reads: methods for alignment and assembly

21 January 2018

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A survey of sequence alignment algorithms for next-generation sequencing

21 January 2018

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Identification of common molecular subsequences

21 January 2018

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Computational methods for transcriptome annotation and quantification using RNA-seq

21 January 2018

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Fast and accurate long-read alignment with Burrows-Wheeler transform

21 January 2018

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Adaptive seeds tame genomic sequence comparison

21 January 2018

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Compressed indexing and local alignment of DNA.

21 January 2018

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Fast gapped-read alignment with Bowtie 2

21 January 2018

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

21 January 2018

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

21 January 2018

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Cancer genome sequencing: a review

21 January 2018

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TopHat: discovering splice junctions with RNA-Seq

21 January 2018

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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

21 January 2018

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The author file: Paul Bertone

21 January 2018

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Understanding mechanisms underlying human gene expression variation with RNA sequencing

21 January 2018

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

21 January 2018

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FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions.

21 January 2018

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Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.

21 January 2018

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SeqEntropy: genome-wide assessment of repeats for short read sequencing

21 January 2018

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Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data

21 January 2018

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

21 January 2018

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BM-map: Bayesian mapping of multireads for next-generation sequencing data

21 January 2018

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Estimation of alternative splicing isoform frequencies from RNA-Seq data

21 January 2018

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GC-content normalization for RNA-Seq data

21 January 2018

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Summarizing and correcting the GC content bias in high-throughput sequencing

21 January 2018

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Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

21 January 2018

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

21 January 2018

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Transcript length bias in RNA-seq data confounds systems biology

21 January 2018

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Comparative studies of de novo assembly tools for next-generation sequencing technologies

21 January 2018

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

21 January 2018

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Exploration, normalization, and summaries of high density oligonucleotide array probe level data

21 January 2018

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

21 January 2018

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Differential expression analysis for sequence count data

21 January 2018

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Revisiting global gene expression analysis

21 January 2018

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Length bias correction for RNA-seq data in gene set analyses

21 January 2018

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

21 January 2018

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Bias detection and correction in RNA-Sequencing data

21 January 2018

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

21 January 2018

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Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

21 January 2018

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Differential expression in RNA-seq: a matter of depth

21 January 2018

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

21 January 2018

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

21 January 2018

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Statistical inferences for isoform expression in RNA-Seq

21 January 2018

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Technical and biological variance structure in mRNA-Seq data: life in the real world

21 January 2018

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

21 January 2018

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

21 January 2018

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

21 January 2018

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

21 January 2018

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Sequencing technology does not eliminate biological variability

21 January 2018

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

21 January 2018

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Detecting differential usage of exons from RNA-seq data

21 January 2018

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A window into third-generation sequencing

21 January 2018

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21 January 2018

Identifiers

DOI

10.1093/BFGP/ELU035

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27 June 2017

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