examples/README.md

In ergonyc/omicser: NDCN Omics Browser

Example files for omicser development

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.

ergonyc/omicser documentation built on June 15, 2022, 3:02 p.m.