F1000Research · 2022 · 10 citations · 52 references
Life SciencesBioinformaticsMolecular BiologyGene ExpressionGenomicsTranscriptomicsAlternative SplicingBulk Rna SequencingDifferential Expression AnalysisRna Sequencing AnalysisSingle-cell Rna Sequencing AnalysisSingle-cell TranscriptomicsDifferential Splicing AnalysisDifferential Transcript ExpressionFalse Discovery ControlFalse Discovery RateFalse Discovery Rate ControlSingle-cell Rna SequencingTranscriptome ProfilingTranscripts
<ns3:p> Alternative splicing produces multiple functional transcripts from a single gene. Dysregulation of splicing is known to be associated with disease and as a hallmark of cancer. Existing tools for differential transcript usage (DTU) analysis either lack in performance, cannot account for complex experimental designs or do not scale to massive single-cell transcriptome sequencing (scRNA-seq) datasets. We introduce <ns3:italic>satuRn</ns3:italic> , a fast and flexible quasi-binomial generalized linear modelling framework that is on par with the best performing DTU methods from the bulk RNA-seq realm, while providing good false discovery rate control, addressing complex experimental designs, and scaling to scRNA-seq applications. </ns3:p>
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STAR: ultrafast universal RNA-seq aligner
Alexander Dobin, Carrie Davis, Felix Schlesinger et al. · Bioinformatics · 2012 · 56.2K citations · Full text