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NACHO: NanoString Quality Control Dashboard

NanoString nCounter data are gene expression assays where there is no need for the use of enzymes or amplification protocols and work with fluorescent barcodes (Geiss et al. (2018) <doi:10.1038/nbt1385>). Each barcode is assigned a messenger-RNA/micro-RNA (mRNA/miRNA) which after bonding with its target can be counted. As a result each count of a specific barcode represents the presence of its target mRNA/miRNA. 'NACHO' (NAnoString quality Control dasHbOard) is able to analyse 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.

Version: 2.0.6
Depends: R (≥ 3.6.0)
Imports: utils, data.table, ggplot2 (≥ 3.3.0), ggforce (≥ 0.3.1), ggrepel (≥ 0.8.1), knitr (≥ 1.25), rmarkdown (≥ 1.16), shiny (≥ 1.4.0), shinyWidgets (≥ 0.4.9)
Suggests: roxygen2 (≥ 7.2.0), testthat (≥ 2.2.1), covr (≥ 3.3.2), Biobase, GEOquery, limma
Published: 2024-01-12
DOI: 10.32614/CRAN.package.NACHO
Author: Mickaël Canouil ORCID iD [aut, cre], Roderick Slieker ORCID iD [aut], Gerard Bouland [aut]
Maintainer: Mickaël Canouil <pro at mickael.canouil.dev>
BugReports: https://github.com/mcanouil/NACHO/issues
License: GPL-3
URL: https://github.com/mcanouil/NACHO/, https://m.canouil.dev/NACHO/
NeedsCompilation: no
SystemRequirements: pandoc (>= 1.14), pandoc-citeproc
Citation: NACHO citation info
Materials: README NEWS
In views: Omics
CRAN checks: NACHO results

Documentation:

Reference manual: NACHO.pdf
Vignettes: NACHO-analysis
NACHO

Downloads:

Package source: NACHO_2.0.6.tar.gz
Windows binaries: r-devel: NACHO_2.0.6.zip, r-release: NACHO_2.0.6.zip, r-oldrel: NACHO_2.0.6.zip
macOS binaries: r-release (arm64): NACHO_2.0.6.tgz, r-oldrel (arm64): NACHO_2.0.6.tgz, r-release (x86_64): NACHO_2.0.6.tgz, r-oldrel (x86_64): NACHO_2.0.6.tgz
Old sources: NACHO archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=NACHO to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.