Nature Methods · 2017 · 13.7K citations · 28 references
Life SciencesBioinformaticsMolecular BiologyGene ExpressionGene Expression AnalysisTranscriptomicsDifferential Gene Expression AnalysisTranscriptome AnnotationTranscriptomic AnalysisTranscriptomics In FishDifferential Transcript ExpressionQuantification BiasTranscript QuantificationTranscript-level Expression AnalysisTranscriptome Normalization
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Fast gapped-read alignment with Bowtie 2
Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations
Near-optimal probabilistic RNA-seq quantification
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The Cancer Genome Atlas Pan-Cancer analysis project
John N. Weinstein, Gordon B. Mills, Kenna Shaw et al. · Nature Genetics · 2013 · 9.5K citations · Full text
Transcriptome and genome sequencing uncovers functional variation in humans
Tuuli Lappalainen, Michael Sammeth, Marc R. Friedländer et al. · Nature · 2013 · 2.2K citations · Full text
Improving RNA-Seq expression estimates by correcting for fragment bias
Adam Roberts, Cole Trapnell, Julie Donaghey et al. · Genome biology · 2011 · 1.8K citations · Full text