Reproducible RNA-seq analysis using recount2

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce

(2016) Abhinav Nellore et al.   BIOINFORMATICS

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Data-driven hypothesis weighting increases detection power in genome-scale multiple testing

(2016) Nikolaos Ignatiadis et al.   NATURE METHODS

Flexible expressed region analysis for RNA-seq withderfinder

(2016) Leonardo Collado-Torres et al.   NUCLEIC ACIDS RESEARCH

A cloud-based workflow to quantify transcript-expression levels in public cancer compendia

(2016) PJ Tatlow et al.   Scientific Reports

Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results

(2015) Mumtahena Rahman et al.   BIOINFORMATICS

Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

(2015) Robert Petryszak et al.   NUCLEIC ACIDS RESEARCH

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data

(2015) Praveen Kumar Raj Kumar et al.   Scientific Reports

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

(2014) Yael Haberman et al.   JOURNAL OF CLINICAL INVESTIGATION

A nineteen gene-based risk score classifier predicts prognosis of colorectal cancer patients

(2014) Seon-Kyu Kim et al.   Molecular Oncology

Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors

(2014) Gerald Goh et al.   NATURE GENETICS

Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans

(2014) John G. Gibbons et al.   Nature Communications

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

(2014) Charity W Law et al.   GENOME BIOLOGY

Transcriptome profiling of human hippocampus dentate gyrus granule cells in mental illness

(2014) R Kohen et al.   Translational Psychiatry

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

An Integrated Model of the Transcriptome of HER2-Positive Breast Cancer

(2013) Krishna R. Kalari et al.   PLoS One

RNA sequencing of cancer reveals novel splicing alterations

(2013) Jeyanthy Eswaran et al.   Scientific Reports

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Utilizing RNA-Seq data for de novo coexpression network inference

(2012) Ovidiu D. Iancu et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome

(2012) Cornelis A Albers et al.   NATURE GENETICS

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

(2012) Intawat Nookaew et al.   NUCLEIC ACIDS RESEARCH

ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets

(2011) Alyssa C Frazee et al.   BMC BIOINFORMATICS

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH