Overview

NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data.
NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes.
Each barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target.
As a result each count of a specific barcode represents the presence of its target mRNA/miRNA.

NACHO is able to load, visualise and normalise the exported NanoString nCounter data and facilitates the user in performing a quality control.
NACHO does this by visualising quality control metrics, expression of control genes, principal components and sample specific size factors in an interactive web application.

With the use of two functions, RCC files are summarised and visualised, namely: summarise() and visualise().

  • The summarise() function is used to preprocess the data.
  • The visualise() function initiates a RStudio Shiny-based dashboard that visualises all relevant QC plots.

NACHO also includes a function normalise(), which calculates sample specific size factors and normalises the data.

  • The normalise() function creates a list in which your settings, the raw counts and normalised counts are stored.

For more vignette("NACHO")