If you would like to test the NDCN Omics Browser with example data, we recommend starting with our example script for PBMC data from 10 Genomics.

Additional scripts include:

• install_script.R: installs R and Python packages, creates environment
• assert_python_script.R: short script for asserting that we are using the configured python environment via reticulate
• example curation scripts for various data types:
  • proteomics_curate_and_config.R: proteomics
  • pbmc3k_curate_and_config.R: single-cell transcriptomics
  • COMING SOON: lipids_curate_and_config.R: lipidomics
• run_browser_script.R: runs the NDCN omics browser via various incantations

Example files include:

• raw_data/ and test_db/: placeholders for locations to put data and database files, respectively

See also:

• app_config.yml: This is an example configuration file for a browser with multiple databases
• dev_run_browser_script.R: shows how to load the repo locally and run the browser, as in a development installation via a cloned repo
• download_examples_script.R: short script which will download and extract just the examples/ directory from the omicser directory.

A short installation & configuration tutorial video is also available which roughly follows this sequence of vignettes:

Files not listed here are used by project developers and are not intended for other users.