README.md

In NACHO: NanoString Quality Control Dashboard

NAnostring quality Control dasHbOard

Installation

# Install NACHO from CRAN:
install.packages("NACHO")

# Or the development version from GitHub:
# install.packages("remotes")
remotes::install_github("mcanouil/NACHO")

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: load_rcc() and visualise().

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

NACHO also includes a function normalise(), which (re)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.

In addition (since v0.6.0) NACHO includes two (three) additional functions:

• The render() function renders a full quality-control report (HTML) based on the results of a call to load_rcc() or normalise() (using print() in a Rmarkdown chunk).
• The autoplot() function draws any quality-control metrics from visualise() and render().

For more vignette("NACHO") and vignette("NACHO-analysis").

Shiny Application (demo)

shiny::runApp(system.file("app", package = "NACHO"))

visualise(GSE74821)

Citing NACHO

Canouil M, Bouland GA, Bonnefond A, Froguel P, Hart L, Slieker R (2019). “NACHO: an R package for quality control of NanoString nCounter data.” Bioinformatics. ISSN 1367-4803, doi:10.1093/bioinformatics/btz647.

@Article{,
  title = {{NACHO}: an {R} package for quality control of {NanoString} {nCounter} data},
  author = {Mickaël Canouil and Gerard A. Bouland and Amélie Bonnefond and Philippe Froguel and Leen Hart and Roderick Slieker},
  journal = {Bioinformatics},
  address = {Oxford, England},
  year = {2019},
  month = {aug},
  issn = {1367-4803},
  doi = {10.1093/bioinformatics/btz647},
}

Getting help

If you encounter a clear bug, please file a minimal reproducible example on github. For questions and other discussion, please contact the package maintainer.

Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

NACHO documentation built on May 29, 2024, 2:05 a.m.