Analysis Pipelines

Arkas – Rapid reproducible RNA-Seq analysis

rna-seq

The recently introduced Kallisto pseudoaligner has radically simplified the quantification of transcripts in RNA-sequencing experiments.  Researchers from the Keck School of Medicine of USC offer cloud-scale RNAseq pipelines Arkas-Quantification, which deploys Kallisto for parallel cloud computations, and Arkas-Analysis, which annotates ...

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Reproducible Bioinformatics Project

Reproducible research is a key component of the scientific method and represents the ability of repeating an experiment in any place with any person. A study can be truly reproducible when it satisfies at least the following three criteria. – ...

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Correcting droplet-based single-cell RNA-seq experiments

rna-seq

Single-cell RNA-seq protocols provide powerful means for examining the gamut of cell types and transcriptional states that comprise complex biological tissues. Recently-developed approaches based on droplet microfluidics, such as inDrop or Drop-seq, use massively multiplexed barcoding to enable simultaneous measurements ...

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Unleash the power within RNA-seq

RNA-sequencing (RNA-seq) is an essential technique for transcriptome studies, hundreds of analysis tools have been developed since it was debuted. Although recent efforts have attempted to assess the latest available tools, they have not evaluated the analysis workflows comprehensively to ...

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