Welcome to the documentation for TRANSPIRE

TRANSPIRE is a Python package for TRanslocation ANalysis of SPatIal pRotEomics data.

QUICKSTART

Installation and depedencies

To install TRANSPIRE, clone or download the GitHub repo and install the package using pip install . from the top-level directory of the package.

Dependencies

TRANSPIRE relies heavily on Pandas for data manipulation, in addition to GPFlow and Tensorflow for building and training Gaussian Process Classifiers.

Given the heavy dependence on Pandas, we recommend that users have, at least, a baseline knowledge of this package.

Documentation contents

The Basics:

• TRANSPIRE Installation
• Steps required to run an analysis with TRANSPIRE

Examples and tutorials:

• Importing and manipulating data for TRANSPIRE analysis
• Hyperparameter optimization
• Final model fitting
• Post-processing of TRANSPIRE results

API:

• TRANSPIRE API
  • TRANSPIRE.data
  • TRANSPIRE.training
  • TRANSPIRE.performance
  • TRANSPIRE.cotranslocation
  • TRANSPIRE.go_enrichment
  • TRANSPIRE.visualization
  • TRANSPIRE.utils

Indices and tables

• Index
• Module Index