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:
NACHO_2.0.6.9000.tar.gz
NACHO_2.0.6.9000.zip(r-4.5)NACHO_2.0.6.9000.zip(r-4.4)NACHO_2.0.6.9000.zip(r-4.3)
NACHO_2.0.6.9000.tgz(r-4.4-any)NACHO_2.0.6.9000.tgz(r-4.3-any)
NACHO_2.0.6.9000.tar.gz(r-4.5-noble)NACHO_2.0.6.9000.tar.gz(r-4.4-noble)
NACHO_2.0.6.9000.tgz(r-4.4-emscripten)NACHO_2.0.6.9000.tgz(r-4.3-emscripten)
NACHO.pdf |NACHO.html✨
NACHO/json (API)
NEWS
| # 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
- GSE74821 - A "nacho" object containing 20 samples of GSE74821 dataset
mirnamrnananostringnormalisationquality-controlshiny
Last updated 10 months agofrom:7c2b47df9c. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 08 2024 |
| R-4.5-win | OK | Oct 08 2024 |
| R-4.5-linux | OK | Oct 08 2024 |
| R-4.4-win | OK | Oct 08 2024 |
| R-4.4-mac | OK | Oct 08 2024 |
| R-4.3-win | OK | Oct 08 2024 |
| R-4.3-mac | OK | Oct 08 2024 |
Exports:autoplotcheck_outliersdeployload_rccnormalisenormalizerendervisualisevisualize
Dependencies:base64encbslibcachemclicolorspacecommonmarkcpp11crayondata.tabledigestevaluatefansifarverfastmapfontawesomefsggforceggplot2ggrepelgluegtablehighrhtmltoolshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigpolyclippromisesR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownsassscalesshinyshinyWidgetssourcetoolssystemfontstibbletidyselecttinytextweenrutf8vctrsviridisLitewithrxfunxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Plot quality-control metrics and thresholds of a "nacho" object | autoplot.nacho |
| Annotate a "nacho" object for outliers | check_outliers |
| Deploy (copy) the shiny application to the specified directory | deploy |
| A "nacho" object containing 20 samples of GSE74821 dataset | GSE74821 |
| Produce a "nacho" object from RCC NanoString files | load_rcc |
| (re)Normalise a "nacho" object | normalise normalize |
| Print method for "nacho" object | print.nacho |
| Render a HTML report of a "nacho" object | render |
| Visualise quality-control metrics of a "nacho" object | visualise visualize |
