Welcome to COMPASS’s documentation!¶
COMPASS (COMpendia Programmatic Access Support Software) is a software layer that provides a GraphQL endpoint to query compendia built using COMMAND>_ technology. COMPASS is meant to be the barebone interface on top of a compendium database and it is usually preferable to query the database using the Python package pyCOMPASS or the R package rCOMPASS for data analysis purposes.
Note
VESPUCCI, the Vitis vinifera cross-platform expression compendium, is accessible using its COMPASS frontend. Check out the use cases!
Table of Contents
- Quick start
- How To
- GET available compendia
- GET compendium data sources
- GET platform information
- GET platform types
- GET experiments information
- GET sample annotation
- GET biological feature annotations
- GET ontology structure
- GET samples annotation triples
- GET sample via SPARQL query
- GET samples by experiment access id
- GET sample by access id
- GET sample set by name
- GET sample set by sample id
- GET sample raw data
- GET biological feature by name
- GET biological feature annotation triples
- CREATE MODULE with biological features and sample sets
- GET available PLOT methods
- PLOT DISTRIBUTION of coexpressed sample sets GIVEN biological features
- PLOT HEATMAP GIVEN a module
- PLOT NETWORK of coexpression GIVEN a module
- GET THE RANKING methods for sample sets and biological features
- GET THE available NORMALIZATION methods for a compendium version
- RANKS sample sets or biological features GIVEN biological features or sample sets respectively
- Deploy COMPASS
Contribute & Support¶
Author¶
To send me an e-mail about anything else related to COMPASS write to
License¶
The project is licensed under the GPLv3 license.