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Implementation of depth calculation methods for genomics data

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statdepth: Depth Calculation Methods

Read the docs at https://statdepth.readthedocs.io/en/latest/.

This package implements depth calculation and visualization methods for univariate time series data, multivariate time series data, and pointcloud data. This README will now mostly be development information. To see how to use the package, visit the documentation at the link above.

Development

To install from pip, run

pip install statdepth

To install locally, run

pip install .

Or to install directly from this repo,

pip install git+https://github.com/braingeneers/functional_depth_methods

To set up the development environment as a Conda env, run

conda env create --file environment.yml

This code is written in Python, with most methods written in Numpy. It also uses numba, a high performance Python compiler. Numba-compiled numerical algorithms in Python can approach the speeds of C or FORTRAN, so this should remove any speed issues Python has.

Depending on how this ends up being used, dask may also be implemented for parallelization.

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