pyprobound

Python implementation of ProBound.

Modules

pyprobound.aggregate	Weighted sum over an aggregate of different binding modes.
pyprobound.alphabets	Alphabets for encoding sequences into tensors.
pyprobound.base	Base classes for typing and sequential optimization procedure encoding.
pyprobound.containers	PyTorch container implementations to fix buffer registration and typing.
pyprobound.cooperativity	Cooperativity between two binding modes.
pyprobound.experiment	Experiment class modeling a CountTable.
pyprobound.external	Import models from ProBound, MotifCentral, JASPAR, and HOCOMOCO.
pyprobound.fitting	Curve fitting to independent validation data.
pyprobound.layers	Implementation of binding mode layers.
pyprobound.loss	Loss components.
pyprobound.mode	Definition of a binding mode as a series of layers applied sequentially.
pyprobound.optimizer	Optimizer of BaseLoss.
pyprobound.plotting	Module of miscellaneous plotting functions.
pyprobound.rounds	Selection layers corresponding to sequencing rounds / CountTable columns.
pyprobound.table	Module for loading and scoring count tables and sequences.
pyprobound.utils	Typed helper functions.