In UofABioinformaticsHub/fastqcRShiny: Shiny App for loading multiple FastQC reports

knitr::opts_chunk$set(message = FALSE, warning = FALSE, eval=FALSE)
fileDir <- system.file("vignettes", package = "fastqcRShiny")

Fast usage

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

library(ngsReports)
library(ngsReportsShinyApp)

fileDir <- 
files <- list.files(fileDir, pattern = "fastqc.zip$", full.names = TRUE)

fastqcShiny()

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

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

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.

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.

UofABioinformaticsHub/fastqcRShiny documentation built on June 10, 2021, 10:39 p.m.