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NanoString quality control dashboard

From RCC files to a quality-control report in three calls.

NACHO reads NanoString nCounter data, flags the samples that fail quality control and normalises the counts. You can then share the result as an interactive app or as a report.

Get started See a report 
install.packages("NACHO")
Other ways to install
Short recording of the NACHO app on the example data. The summary strip changes when the field of view threshold moves and one sample is flagged. The recording then shows the Samples, Normalisation, Batch and Export pages.

NACHO

Step 1

Load

Read the RCC files and a sample sheet. One call computes the quality-control metrics and normalises the counts.

load_rcc()

Step 2

Check

Look at each metric in the app, or plot one metric in your own script.

visualise() autoplot()

Step 3

Share

Write an HTML or PDF report that records the decisions you made.

render()

The quality-control metrics page of the NACHO app, with a box plot for each metric and the limits drawn as dashed lines.
The quality-control metrics page of the NACHO app, with a box plot for each metric and the limits drawn as dashed lines.

Shiny app

See every sample, change every limit

  • The summary strip counts the flagged samples while you move a limit.
  • Select a sample once, and every plot outlines it.
  • Separate pages show the control probes, the normalisation and the batch effects.
  • The Export page writes the report from the app.
visualise(nacho)

Explore quality control in the app

The top of the HTML report, with the study header and the decision summary for one flagged sample.
The top of the HTML report, with the study header and the decision summary for one flagged sample.
The cover page of the PDF report.
The cover page of the PDF report.
A page of the PDF report, with the running header, the decision summary and the page footer.
A page of the PDF report, with the running header, the decision summary and the page footer.

Quarto report

A quality-control record you can hand over

  • The same nacho object gives an HTML report or a PDF report.
  • The decision summary comes first: which samples fail, and why.
  • Figures have numbers and captions, and tables are accessible.
  • A methods section records the settings and the software versions.
render(nacho, format = "typst")

Write a quality-control report

Box plot of the binding density of each cartridge, with the limits of the quality control drawn as dashed lines.
Box plot of the binding density of each cartridge, with the limits of the quality control drawn as dashed lines.

Analysis

Part of your R workflow

Analyse a GEO study Moving from NACHO 2

Installation

Install the release from CRAN:

If you want the development version without an extra package, install it from R-universe:

install.packages(
  "NACHO",
  repos = c("https://mcanouil.r-universe.dev", "https://cloud.r-project.org")
)

If you want the latest commit, install it from GitHub with pak:

# install.packages("pak")
pak::pak("mcanouil/NACHO")

Cite and get help

If you use NACHO in your work, cite the article in Bioinformatics. To report a bug, open an issue on GitHub with a minimal reproducible example. This project has a Contributor Code of Conduct.