Package index • NACHO

Load and normalise

Read RCC files, compute quality-control metrics and normalise counts.

load_rcc(): Produce a "nacho" object from RCC NanoString files
read_nacho(): Read a saved NACHO object
upgrade_nacho(): Convert a NACHO 2 object to NACHO 3
as_summarized_experiment() as_nacho(): Convert between nacho objects and Bioconductor containers
nacho_thresholds(): Quality-control thresholds
write_thresholds() read_thresholds(): Write and read quality-control thresholds
normalise(): (Re)normalise a nacho object
exclude_outliers(): Drop outliers and normalise the other samples again
housekeeping_stability(): Rank genes by expression stability
suggest_ruv_k(): Suggest how many unwanted factors RUVg should remove
batch_diagnostics(): Batch and confounding diagnostics

Explore quality control interactively, plot a single metric, or write a full report.

visualise(): Explore and tune quality control in the NACHO app
autoplot.nacho: Plot the quality control of a nacho object
nacho-methods: Basic methods for a nacho object
nacho_counts() nacho_samples() nacho_probes() nacho_qc(): Get the content of a nacho object
filter_detected(): Keep genes detected in enough samples
render(): Render the quality-control report of a nacho object