rnaxqc

rnaxqc

Shiny based Quality Control tool for expression counts in the context of the experiment.

rnaxqc is a tool that helps to inspect the quality of counting reads from RNA sequencing experiment. The counting statistics is presented within a context of the experiment. The experiment design is described in the design table file.

Input

There are two kinds of input necessary for this app two work.

• design table file
• count table(s)

They should be located in data directory. It is important that sampleids (first column in design table) match column names in cout table(s).

design table file (design.txt)

The design file should be in is meant to describe the experimental setup.

Design table is tab delimited file with a header. First 3 columns have to be sampleid, barcode and runid. There can by any number of columns. Data in the columns should be categorical, not numerical. Every row is a single sample.

count table (CountTable_{RNA_species}.txt)

Count table is a tab delimited file with a header.

First column is an RNA species, each of remaining columns is one sample. {RNA_species} in the name of the file is the name of the type of RNA (piRNA, miRNA, snoRNA etc.) this name is used in the visualisation.

Running the app

To run the app start R from inside the analysis directory and execute:

shiny::runApp()

R will return the port number on which shiny.app is available. You can access it using a modern web browser (latest Chrome or Firefox) at localhost:port where port is a port number returned by the command.