ngsReports shiny app user guide

Christopher Ward1*, Hien To2 and Steve Pederson2**

1School of Biological Sciences, University of Adelaide
2Bioinformatics Hub, University of Adelaide

*christopher.ward@adelaide.edu.au
**stephen.pederson@adelaide.edu.au

Contents

1 Fast usage

The shiny app can be run after loading the base package ngsReports and the shiny app shinyNgsreports.

This will open the shiny app. Files can then be imported by clicking the Choose Files button.

Choosing files from within the shiny app

FastQC modules can then be selected using the sidebar. Each module has a summary of PASS/WARN/FAIL status across all FastQC files loaded.

Selecting a module

After selecting a module, in this case the GC Content module, plots are rendered and shown for all samples in heatmap format. A single sample can then be selected by clicking the sidebar on the heatmap.

Data in both the heatmap and line plot can be hovered over to display a tooltip containing x and y axis information and module value.

Tooltip on hover

2 Outputting the default HTML report from the shiny app

The default HTML report can also be run from the shiny app by selecting the last tab from the sidebar. -Omic type (i.e. Genomic or Transciptomic) can then be selected along with the species of interest. The directory containing fasqc files to construct a report for can then be selected using the elipsis on the choose files button.

Tooltip on hover