Type: Package
Package: NACHO
Title: NanoString Quality Control Dashboard
Version: 3.0.0
Authors@R: 
    c(person(given = "Mickaël",
             family = "Canouil",
             role = c("aut", "cre"),
             email = "pro@mickael.canouil.dev",
             comment = c(ORCID = "0000-0002-3396-4549")),
      person(given = "Roderick",
             family = "Slieker",
             role = "aut",
             email = "R.C.Slieker@lumc.nl",
             comment = c(ORCID = "0000-0003-0961-9152")),
      person(given = "Gerard",
             family = "Bouland",
             role = "aut",
             email = "G.A.Bouland@lumc.nl"))
Description: 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.
License: GPL-3
Copyright: See file inst/COPYRIGHTS.
URL: https://github.com/mcanouil/NACHO/, https://m.canouil.dev/NACHO/
BugReports: https://github.com/mcanouil/NACHO/issues
Depends: R (>= 4.3)
Imports: methods, utils, grDevices, bslib (>= 0.10.0), brand.yml (>=
        0.1.0), cli (>= 3.6.0), data.table, ggplot2 (>= 4.0.0), ggforce
        (>= 0.5.0), ggrepel (>= 0.9.6), htmltools (>= 0.5.9), promises
        (>= 1.3.2), rlang (>= 1.1.0), S7 (>= 0.2.2), scales (>= 1.4.0),
        shiny (>= 1.11.0), yaml (>= 2.3.12)
Suggests: chromote (>= 0.5.1), colorspace (>= 2.1-3), gdtools (>=
        0.5.2), ggiraph (>= 0.9.6), jsonlite (>= 2.0.0), knitr (>=
        1.39), later, mirai (>= 2.7.3), parallel, png (>= 0.1-9),
        quarto (>= 1.5.1), reactable (>= 0.4.5), rmarkdown (>= 1.16),
        roxygen2 (>= 8.1.0), shinytest2 (>= 0.5.1), testthat (>=
        3.1.5), vdiffr (>= 1.0.9), withr, covr (>= 3.3.2), Biobase,
        GEOquery, limma, NanoStringNCTools, NormqPCR, RUVSeq,
        S4Vectors, SummarizedExperiment
biocViews:
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
LazyData: true
SystemRequirements: Quarto command-line interface (>= 1.9.18), pandoc
        (>= 2.11)
Config/Needs/website: pdftools
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Collate: 'GSE74821.R' 'NACHO-package.R' 'thresholds.R' 'qc.R'
        'nacho-class.R' 'accessors.R' 'daemon.R' 'render.R'
        'mod_export.R' 'qc-table.R' 'report.R' 'mod_qc_plot.R'
        'mod_batch.R' 'mod_outliers.R' 'mod_overview.R'
        'mod_thresholds.R' 'load_rcc.R' 'mod_data.R' 'tour.R' 'app.R'
        'autoplot.R' 'stability.R' 'ruv.R' 'mirna.R' 'batch.R'
        'brand.R' 'conditions.R' 'deploy.R' 'detection.R' 'interop.R'
        'methods.R' 'normalise.R' 'plot_worker.R' 'read_nacho.R'
        'read_rcc.R' 'utils.R' 'visualise.R' 'zzz.R'
NeedsCompilation: no
Packaged: 2026-11-01 21:14:38 UTC; runner
Author: Mickaël Canouil [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3396-4549>),
  Roderick Slieker [aut] (ORCID: <https://orcid.org/0000-0003-0961-9152>),
  Gerard Bouland [aut]
Maintainer: Mickaël Canouil <pro@mickael.canouil.dev>
Repository: CRAN
Date/Publication: 2026-11-01 21:50:02 UTC
