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Old 01-16-2015, 12:43 PM   #1
Fabien Campagne
Location: New York City

Join Date: Feb 2010
Posts: 39
Default MetaR: a simple language useful for RNA-Seq data analysis


I wanted to introduce MetaR, a language to analyze RNA-Seq data and produce visualizations such as heatmaps. MetaR provides a language simpler to learn and use than R, yet generates full analysis scripts in R, using popular R/Bioconductor packagages (e.g., data.table, EdgeR, pheatmap). We find that on average 1 line of MetaR generates about 5-10 lines of R code. The language offers full auto-completion for table, columns, model or plot names, making it easier for beginners to get started.

Below is a snapshot of an RNA-Seq analysis followed by construction of a heatmap with the MetaR language.

This blog post has more details about motivations and design and links to a video demonstrating how to build a heatmap from a table of read counts with MetaR. For the technically inclined, MetaR is a composable language, which means that it is easy to extend with new instructions, expressions, or other language constructs, in ways that are not practical with traditional languages. You can even extend the language as you are writing a new script and realize you need a new kind of statement.

Last edited by Fabien Campagne; 01-22-2015 at 05:25 AM. Reason: Replaced the snapshot with a version that illustrates that a MetaR analysis is not text, but an interactive user interface.
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data analysis, language workbench, metar

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