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RNA-Seq Gene Profiling - A Systematic Empirical Comparison

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The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data

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

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The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

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Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

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Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser

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

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Comprehensive genomic characterization of squamous cell lung cancers

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Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

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

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BEDTools: a flexible suite of utilities for comparing genomic features

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

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MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

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Mapping and quantifying mammalian transcriptomes by RNA-Seq

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