Biological sequence analysis for the modern age.
bpnet-lite is a minimal implementation of BPNet, a neural network aimed at interpreting regulatory activity of the genome.
dragonnfruit is a method for analyzing scATAC-seq experiments.
A PyTorch implementation of probabilistic models.
Ledidi is an optimization approach for designing edits to biological sequences.
Transcription Factor MOtif Discovery from Importance SCOres - lite
A rewrite of pomegranate using PyTorch.
yuzu implements a compressed-sensing based approach for speeding up saliency calculations.
Avocado is a package for learning a latent representation of the human epigenome.
apricot is a package for submodular selection of representative sets for machine learning models.
Kiwano is an implementation of an approach for prioritizing epigenomic and transcriptomic experiments.
rambutan is a python wrapper for caffe, aiming to provide a simpler way to define, train, and evaluate models.
Nanopore Data Analysis package. Provides tools for reading data, performing event detection, segmentation, visualization, and analysis using hidden Markov models, and other tools. Designed for the UCSC Nanopore Group.
YAHMM is a HMM package for Python, implemented in Cython for speed.
antz is a bioinformatics package written for python.
YABN is a Bayesian Network package for Python, implemented in Cython for speed.
DISCERN is a method for identifying perturbations between two similar graphs. It takes in samples from two networks, and identifies which features are conditionally dependent on different features between the two