Nanostring Quality Control Dashboard

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Installation

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

# Or the 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: summarise() and visualise().

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

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

For more vignette("NACHO").

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.


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