Unifying cancer and normal RNA sequencing data from different sources

Toil enables reproducible, open source, big biomedical data analyses

(2017) John Vivian et al.   NATURE BIOTECHNOLOGY

MTD: a mammalian transcriptomic database to explore gene expression and regulation

(2016) Xin Sheng et al.   BRIEFINGS IN BIOINFORMATICS

OASIS: web-based platform for exploring cancer multi-omics data

(2016) Julio Fernandez-Banet et al.   NATURE METHODS

Assessing the consistency of public human tissue RNA-seq data sets

(2015) F. Danielsson et al.   BRIEFINGS IN BIOINFORMATICS

The Molecular Taxonomy of Primary Prostate Cancer

(2015) Adam Abeshouse et al.   CELL

Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells

(2015) Jian-Rong Li et al.   NUCLEIC ACIDS RESEARCH

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

(2015) et al.   SCIENCE

mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data

(2015) Huijuan Feng et al.   Nature Communications

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Editorial: NAR Surveys the Past, Present and Future of Restriction Endonucleases

(2013) W. Dynan et al.   NUCLEIC ACIDS RESEARCH

CellFinder: a cell data repository

(2013) Harald Stachelscheid et al.   NUCLEIC ACIDS RESEARCH

Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

(2013) Robert Petryszak et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing

(2012) Markus Krupp et al.   BIOINFORMATICS

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS