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) ). 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.


News

NACHO 0.5.5

Minor improvements and fixes

  • In R/summarise.R, put example in if (interactive()) {...} instead of \dontrun{...}.
  • In R/normalise.R, put example in if (interactive()) {...} instead of \dontrun{...}.
  • In R/visualise.R, put example in if (interactive()) {...} instead of \dontrun{...}.
  • In DESCRIPTION and README, description updated for CRAN, by adding "messenger-RNA/micro-RNA".

NACHO 0.5.4

Minor improvements and fixes

  • In R/normalise.R, add short running example for normalise().
  • In R/visualise.R, add short running example for visualise().
  • In DESCRIPTION, description updated for CRAN, by removing some capital letters and put NACHO between single quotes.

NACHO 0.5.3

Minor improvements and fixes

  • Bold letters for NACHO in title.
  • In DESCRIPTION, title and description updated for CRAN.
  • Add NanoString reference in DESCRIPTION and vignette

NACHO 0.5.2

Minor improvements and fixes

  • In DESCRIPTION, title and description updated for CRAN.

NACHO 0.5.1

Minor improvements and fixes

  • Vignette uses bib file for references.
  • Update URL in DESCRIPTION.

NACHO 0.5.0

New features

  • summarise() imports and pre-process RCC files.
  • normalise() allows to change settings used in summarise() and exclude outliers.
  • visualise() allows customisation of the quality thresholds.
  • Minor changes

Minor improvements and fixes

  • Add a README.
  • Add logo.
  • In summarise(), ssheet_csv can take a data.frame or a csv file.
  • Change in package title with capital letters corresponding to NACHO.
  • Add tests using testthat.

NACHO 0.4.0

  • Fix major errors, bad behaviour and typos.

NACHO 0.3.1

  • Add and fill roxygen documentation.

NACHO 0.3.0

  • Code optimisation in normalise() (and internal functions).
  • visualise() replaces the Shiny app.

NACHO 0.2.2

  • Remove S4 class => Back to list object.

NACHO 0.2.1

  • Rewrite GEO dataset.

NACHO 0.2.0

  • Complete rewrite of summarise() and normalise() (and all internal functions).
  • Add S4 class object.

NACHO 0.1.0

  • First version.

Reference manual

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install.packages("NACHO")

0.5.6 by Mickaël Canouil, 3 months ago


https://mcanouil.github.io/NACHO


Report a bug at https://github.com/mcanouil/NACHO/issues


Browse source code at https://github.com/cran/NACHO


Authors: Mickaël Canouil [aut, cre] , Roderick Slieker [aut] , Gerard Bouland [aut]


Documentation:   PDF Manual  


GPL-3 | file LICENSE license


Imports tibble, dplyr, tidyr, purrr, shiny, scales, ggplot2, ggbeeswarm, ggrepel, ggpubr, gtools

Suggests covr, Biobase, GEOquery, utils, sessioninfo, knitr, rmarkdown, testthat


See at CRAN