Holistic optimization of an RNA-seq workflow for multi-threaded environments

CSAMA 2014: RNA-Seq differential expression workflow

This lab will walk you through an end-to-end RNA-Seq differential expression workflow. We will start from the FASTQ files, align to the reference genome, prepare gene expression values as a count table by counting the sequenced fragments, perform differential gene expression analysis, and visually explore the results. This lab covers the basic introduction. For a more in-depth explanation of th...

BioC2014: RNA-Seq workflow for differential gene expression

This lab will walk you through an end-to-end RNA-Seq differential expression workflow. We will start from the FASTQ files, align to the reference genome, prepare gene expression values as a count table by counting the sequenced fragments, perform differential gene expression analysis, and visually explore the results. This lab covers the basic introduction. For a more in-depth explanation of th...

Static code analysis in multi-threaded environments

Who can understand his errors? Cleanse thou me from secret faults. Preface The notion that software might contain errors dates back to the famous annotations of Lady Ada Lovelace to the description of the Analytical Engine designed by Charles Babbage[36] where she states: " Granted that the actual mechanism [of the Analytic Engine] is unerring in its processes, the cards may give it wrong order...

RNA-Seq workflow: gene-level exploratory analysis and differential expression

Here we walk through an end-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample. We will perform exploratory data analysis (EDA) for quality assessment and to e...

An Architecture for a Multi-threaded