Package index • RiboPilot

Start a project

Create a project, open the app, and add or update samples.

new_test_project(): Initialize a RiboPilot test project
new_project(): Initialize a new RiboPilot project
run_app() RiboPilot(): Open the RiboPilot app
add_samples(): Add samples to an existing project
update_sample_metadata(): Update metadata for existing samples
backwards_compatibility(): Update an old project to the installed RiboPilot

Sample metadata

Fetch specimen records from GEOME, GBIF, and NCBI, and choose what to compare.

fetch_geome(): Fetch GEOME metadata for project samples
fetch_gbif(): Fetch GBIF occurrence metadata for project samples
fetch_ncbi(): Fetch NCBI BioSample and BioProject metadata for project samples
remove_metadata(): Remove fetched GEOME, GBIF, and NCBI metadata
set_metadata_columns(): Choose which mapping-file columns are compared with GEOME, GBIF, and NCBI

Reference databases

Build a reference database from R, and find the shared reference folder.

build_reference_db(): Build a clade nuclear-rDNA reference database (GetOrganelle seeds + labels)
ribopilot_ref_dir(): Default directory for user-built reference databases

Clusters

Set up a profile for your cluster’s scheduler.

generate_config(): Generate and save a reusable cluster config profile
hydra_setup(): Configure the R session environment for the NMNH Hydra cluster

Export

Write GenBank submission files without the app.

export_project(): Export a project's locked units as GenBank bundles