NanoString Quality Control Dashboard

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Documentation for package ‘NACHO’ version 3.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

as_nacho	Convert between nacho objects and Bioconductor containers
as_summarized_experiment	Convert between nacho objects and Bioconductor containers
autoplot.nacho	Plot the quality control of a nacho object
batch_diagnostics	Batch and confounding diagnostics
deploy	Deploy (copy) the Shiny application to the specified directory
exclude_outliers	Drop outliers and normalise the other samples again
filter_detected	Keep genes detected in enough samples
GSE74821	A "nacho" object with 48 samples from the GSE74821 dataset
housekeeping_stability	Rank genes by expression stability
load_rcc	Produce a "nacho" object from RCC NanoString files
nacho-accessors	Get the content of a nacho object
nacho-methods	Basic methods for a nacho object
nacho_app	Run the NACHO app
nacho_counts	Get the content of a nacho object
nacho_probes	Get the content of a nacho object
nacho_qc	Get the content of a nacho object
nacho_samples	Get the content of a nacho object
nacho_thresholds	Quality-control thresholds
normalise	(Re)normalise a nacho object
normalize	(Re)normalise a nacho object
read_nacho	Read a saved NACHO object
read_thresholds	Write and read quality-control thresholds
render	Render the quality-control report of a nacho object
suggest_ruv_k	Suggest how many unwanted factors RUVg should remove
upgrade_nacho	Convert a NACHO 2 object to NACHO 3
visualise	Explore and tune quality control in the NACHO app
visualize	Explore and tune quality control in the NACHO app
write_thresholds	Write and read quality-control thresholds