README.md

In freezecoder/ngsrview: An R Shiny Module for viewing common NGS file formats

ngsrview

Simple file format viewer for NGS variant data

Description

Use this package to take a quick peak/inspection at the following types of files

1. Gemini TSV output files
2. snpEff TSV output files
3. AnnoVCF TSV output files

Installation

library(devtools)
install_github("freezecoder/ngsrview")

Usage

library(shiny)
library(DT)
library(shinyjs)
library(data.table)
library(googleVis)
library(ggplot2)
library(rjson)

genericNGSTestApp()

Open a browser to the port the shiny app is running, then upload some files.

Download this input file and use it as an input to the viewer. The file should have a .vtbl.tsv extension so it is recognized as containing variant information.

wget https://raw.githubusercontent.com/freezecoder/ngsrview/master/inst/extdata/sample_vtable.tsv -O sample.vtbl.tsv

Use the file upload button to upload this file and see the different result tabs in the viewer

freezecoder/ngsrview documentation built on Jan. 28, 2020, 9:29 p.m.