CDNMp2c overview

Vincent J. Carey, stvjc at channing.harvard.edu

May 04, 2023

Purpose

Provide general access to use cases for a transition to cloud computing for a research lab focused on lung disease genetics and personalized genomic medicine

See the “Articles” tab for details. To get the flavor of test projects, we have

Carey group

BiocHail

We have an R package in Bioconductor that runs through the following topics (this is just a screenshot, visit BiocHail at Bioconductor for details):

Project activity: Log into cloud instance, start Rstudio, work with BiocHail without user-level installation. Requires access to a 6GB Hail MatrixTable, preferably shared. Objective: Should we use MatrixTables and their annotation to represent our GWAS?

BiocT2T

We want to accelerate adoption of the new telomere-to-telomere genome reference. To get the flavor we have an app that looks like:

Full details at VJC’s pkgdown site

Project activity: Log into cloud instance, start Rstudio, work with variants in the T2T calls of 3202 1000 genomes samples. Subset to samples with transcriptomic data in GEUVADIS and with DNAse-seq data from Degner 2012 (or updated material on similar topics). Objective: Does the higher-resolution genotyping lead to new insights on molecular QTLs?