Package: NACHO 2.0.6.9000

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.

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

NACHO_2.0.6.9000.tar.gz
NACHO_2.0.6.9000.zip(r-4.7)NACHO_2.0.6.9000.zip(r-4.6)NACHO_2.0.6.9000.zip(r-4.5)
NACHO_2.0.6.9000.tgz(r-4.6-any)NACHO_2.0.6.9000.tgz(r-4.5-any)
NACHO_2.0.6.9000.tar.gz(r-4.7-any)NACHO_2.0.6.9000.tar.gz(r-4.6-any)
NACHO_2.0.6.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
NACHO/json (API)

# Install 'NACHO' in R:
install.packages('NACHO', repos = c('https://mcanouil.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mcanouil/nacho/issues

Pkgdown/docs site:https://m.canouil.dev

Datasets:
  • GSE74821 - A "nacho" object containing 20 samples of GSE74821 dataset

On CRAN:

Conda:

mirnamrnananostringnormalisationquality-controlshiny

5.60 score 9 stars 44 scripts 298 downloads 9 exports 57 dependencies

Last updated from:7c2b47df9c. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK174
source / vignettesOK310
linux-release-x86_64OK173
macos-release-arm64OK96
macos-oldrel-arm64OK137
windows-develOK107
windows-releaseOK115
windows-oldrelOK113
wasm-releaseOK147

Exports:autoplotcheck_outliersdeployload_rccnormalisenormalizerendervisualisevisualize

Dependencies:base64encbslibcachemclicommonmarkcpp11data.tabledigestevaluatefarverfastmapfontawesomefsggforceggplot2ggrepelgluegtablehighrhtmltoolshttpuvisobandjquerylibjsonliteknitrlabelinglaterlifecyclemagrittrMASSmemoisemimeotelpolyclippromisesR6rappdirsRColorBrewerRcpprlangrmarkdownS7sassscalesshinyshinyWidgetssourcetoolssystemfontstidyselecttinytextweenrvctrsviridisLitewithrxfunxtableyaml

NACHO
Installation | Overview | An example | Get NanoString nCounter data | Presummarised data from NACHO | Raw data from GEO | The load_rcc() function | The visualise() function | The normalise() function | The autoplot() function | NACHO as a standalone app | The render() function | References
Rendered fromNACHO.Rmdusingknitr::rmarkdown

Last update: 2022-12-05
Started: 2019-03-15

NACHO Analysis
Installation | Overview | Analyse NanoString data | Load packages | Download GSE70970 from GEO (or use your own data) | Import RCC files | Perform the analyses using limma | Get the phenotypes | Get the normalised counts | Select phenotypes and counts | Perform the analyses using lm (or any other model)
Rendered fromNACHO-analysis.Rmdusingknitr::rmarkdown

Last update: 2022-12-05
Started: 2019-12-31