Bryan Lewis - The `scidb` package for large data and genomics analysis

For our October meeting, we're pleased to host Bryan Lewis once again. He'll show us how to use RStudio, Shiny, and SciDB to demonstrate a few common, real-world genomics analysis workflows in use today by SciDB-R users (full abstract below). Also a big thanks to RStudio (http://www.rstudio.com/) for graciously sponsoring the pizza for the meeting!

Bryan Lewis is Paradigm4's Chief Data Scientist. He is the author of a number of R packages including SciDB-R, and has worked on many performance-related aspects of R. Bryan is an applied mathematician, kayaker, and avid amateur mycologist.

Agenda:

• 6:00 - 6:30pm - Pizza and networking

• 6:30 - 7:30pm - Bryan Lewis - The `scidb` package

Abstract:

R is a powerful system for computation and visualization widely used in biostatistics and analyses of genomic data. An active and engaged research community continuously expands R's capabilities through thousands of available packages on CRAN and Bioconductor.

SciDB is a scalable open-source database used in large omics workloads like the NCBI 1000 genomes project and other genomic variant applications, applications derived from the cancer genome atlas, and more.

The `scidb` package for R available on CRAN lets R researchers use SciDB on very large datasets directly from R without learning a new database query language. Bryan will use RStudio, Shiny, and SciDB to demonstrate a few common, real-world genomics analysis workflows in use today by SciDB-R users. We'll see basic techniques like enrichment problems using fast parallel Fisher tests and also more challenging problems like large-scale correlation and network analysis.