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 
[aut, cre],
Roderick Slieker
[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.html , NACHO.pdf |
| Vignettes: |
NACHO-analysis (source, R code) NACHO (source, R code) |
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:
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