README.md

In vjcitn/lungGen: Genomic contexts of lung-disease associated SNP

title: "lungGen: SNP annotation for lung disease" author: "Vincent J. Carey, stvjc at channing.harvard.edu" date: "r format(Sys.time(), '%B %d, %Y')" vignette: > %\VignetteEngine{knitr::rmarkdown} %\VignetteIndexEntry{lungGen overview} %\VignetteEncoding{UTF-8} output: BiocStyle::html_document: highlight: pygments number_sections: yes theme: united toc: yes

Introduction

We are using a variety of reference resources to characterize genomic context of DNA variants.

lungGen is a prototypical interactive resource to help explore context. Upon installation and attachment of the package, invoking lungGen() produces a browser page for interactive exploration.

Interface components

Overview

Sidebar panel allows selection of phenotype and gene of interest. Phenotype selection filters the GWAS catalog (in this release, limited to GWAS hits on chr17), gene selection is used for transcript model display to be discussed below.

Literature references

Note that a brief summary of all papers cited in the GWAS catalog is provided on the front panel. This will be expanded to support abstract retrieval. Locus-specific links to pubmed are on the next tab.

Locus details

Epigenetic states enclosing loci

Transcript model with predicted phenorelevance scores

vjcitn/lungGen documentation built on May 24, 2019, 8:53 a.m.