xstate: State Analysis for Gene Expression

Developer Usage Notes

1. Execute source setup_env.sh at the directory root
2. Run python codes from the directory src/python

Installation

The installation assumes that you have installed git and anaconda (or miniconda).

• git clone --recurse-submodules https://github.com/uwescience/xstate.git
• cd xstate
• bash setup.sh

Windows users should manually perform the steps in setup.sh.

Usage

For all use cases:

1. Start a new terminal session
2. cd xstate
3. conda activate xstate

When done, conda deactivate xstate

Update the classifiers:

1. From the top level repository directory, python xstate/xstate/python/tools/make_svm_classifier.py. (On windows, use \ instead of /.

Run a classification:

1. Start a new terminal session, change directory to xstate, and activate the virtual environment.
2. From the top level repository directory, python xstate/xstate/python/tools/classify_expression.py <data_file>. (On windows, use \ instead of /. Note: It is assumed that <data file> is in the samples directory under data. To change the directory, use the --dir option.