4.8 Article

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

HTSeq-a Python framework to work with high-throughput sequencing data

Simon Anders et al.

BIOINFORMATICS (2015)

Article Engineering, Aerospace

Phenotypic, genomic, transcriptomic and proteomic changes in Bacillus cereus after a short-term space flight

Longxiang Su et al.

ADVANCES IN SPACE RESEARCH (2014)

Article Biochemical Research Methods

RNA-seq differential expression studies: more sequence or more replication?

Yuwen Liu et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

RNASeqGUI: a GUI for analysing RNA-Seq data

Francesco Russo et al.

BIOINFORMATICS (2014)

Article Biotechnology & Applied Microbiology

LFCseq: a nonparametric approach for differential expression analysis of RNA-seq data

Bingqing Lin et al.

BMC GENOMICS (2014)

Article Biotechnology & Applied Microbiology

Detecting and correcting systematic variation in large-scale RNA sequencing data

Sheng Li et al.

NATURE BIOTECHNOLOGY (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression

Michele A. Busby et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

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

Charlotte Soneson et al.

BMC BIOINFORMATICS (2013)

Article Biochemical Research Methods

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

Marie-Agnes Dillies et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Article Biotechnology & Applied Microbiology

Transcriptome analysis of normal and mantled developing oil palm flower and fruit

Jeremy R. Shearman et al.

GENOMICS (2013)

Article Biochemical Research Methods

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

Simon Anders et al.

NATURE PROTOCOLS (2013)

Article Biochemistry & Molecular Biology

DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions

Guenter Klambauer et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination

Wen-Yu Liu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Health Care Sciences & Services

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

Jun Li et al.

STATISTICAL METHODS IN MEDICAL RESEARCH (2013)

Article Biotechnology & Applied Microbiology

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

Daehwan Kim et al.

GENOME BIOLOGY (2013)

Article Biotechnology & Applied Microbiology

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

Franck Rapaport et al.

GENOME BIOLOGY (2013)

Article Biochemical Research Methods

RSeQC: quality control of RNA-seq experiments

Liguo Wang et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

RNA-SeQC: RNA-seq metrics for quality control and process optimization

David S. DeLuca et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

Qualimap: evaluating next-generation sequencing alignment data

Fernando Garcia-Alcalde et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

Accuracy of RNA-Seq and its dependence on sequencing depth

Guoshuai Cai et al.

BMC BIOINFORMATICS (2012)

Article Biochemistry & Molecular Biology

GENCODE: The reference human genome annotation for The ENCODE Project

Jennifer Harrow et al.

GENOME RESEARCH (2012)

Article Multidisciplinary Sciences

An integrated encyclopedia of DNA elements in the human genome

Ian Dunham et al.

NATURE (2012)

Article Biochemistry & Molecular Biology

Ensembl 2012

Paul Flicek et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

Computer-assisted coloring and illuminating based on a region-tree structure

Renata Nascimento et al.

SPRINGERPLUS (2012)

Article Biochemical Research Methods

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling

Pawel P. Labaj et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

Bias detection and correction in RNA-Sequencing data

Wei Zheng et al.

BMC BIOINFORMATICS (2011)

Article Biochemical Research Methods

GC-Content Normalization for RNA-Seq Data

Davide Risso et al.

BMC BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

Differential expression in RNA-seq: A matter of depth

Sonia Tarazona et al.

GENOME RESEARCH (2011)

Article Biochemical Research Methods

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

Mark D. Robinson et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

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

James H. Bullard et al.

BMC BIOINFORMATICS (2010)

Article Biotechnology & Applied Microbiology

Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance

Ali Bashir et al.

BMC GENOMICS (2010)

Article Genetics & Heredity

Statistical Design and Analysis of RNA Sequencing Data

Paul L. Auer et al.

GENETICS (2010)

Article Biochemical Research Methods

Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human

James R. Wagner et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

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

Matthew D. Young et al.

GENOME BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

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

Mark D. Robinson et al.

GENOME BIOLOGY (2010)

Article Biochemical Research Methods

TopHat: discovering splice junctions with RNA-Seq

Cole Trapnell et al.

BIOINFORMATICS (2009)

Article Biology

Transcript length bias in RNA-seq data confounds systems biology

Alicia Oshlack et al.

BIOLOGY DIRECT (2009)

Review Genetics & Heredity

RNA-Seq: a revolutionary tool for transcriptomics

Zhong Wang et al.

NATURE REVIEWS GENETICS (2009)

Article Biochemistry & Molecular Biology

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

John C. Marioni et al.

GENOME RESEARCH (2008)

Article Biochemical Research Methods

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Ali Mortazavi et al.

NATURE METHODS (2008)

Article Biotechnology & Applied Microbiology

Bioconductor: open software development for computational biology and bioinformatics

RC Gentleman et al.

GENOME BIOLOGY (2004)

Article Statistics & Probability

Empirical Bayes analysis of a microarray experiment

B Efron et al.

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION (2001)