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abada

GUI for analyzing nanopore data, based on the Abada package.

antz

Bioinformatic tools for biologists, made pythonic!

apricot

apricot implements submodular optimization for the purpose of selecting subsets of massive data sets to train machine learning models quickly. See the documentation page: https://apricot-select.readthedocs.io/en/latest/index.html

avocado

Avocado is a multi-scale deep tensor factorization model that learns a latent representation of the human epigenome and enables imputation of epigenomic experiments that have not yet been performed.

awesome-machine-learning

A curated list of awesome Machine Learning frameworks, libraries and software.

blueberry

Inference of the 3D structure of genomes

bpnet-lite

This repository hosts a minimal version of a Python API for BPNet.

constraint_graphs

Repository for the data and associated notebook for the manuscript "Finding the optimal Bayesian network given a constraint graph."

covid-19

Novel Coronavirus (COVID-19) Cases, provided by JHU CSSE

deep-learning-notes

Experiments with Deep Learning

discern

dragonnfruit

A method for analyzing scATAC-seq experiments.

grelu

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

hmmlearn

Hidden Markov Models in Python, with scikit-learn like API

ipython

Repository for my ipython notebooks.

jmschrei.github.io

kantalope

because it can't alope

keras

Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano or TensorFlow.

kiwano

Kiwano implements an approach for prioritizing epigenomic and transcriptomic characterization based on submodular selection and imputed experiments

ledidi

Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.

lifelines

Survival analysis in Python

mxnet

Lightweight, Portable, Flexible Distributed/Mobile Deep Learning with Dynamic, Mutation-aware Dataflow Dep Scheduler; for Python, R, Julia, Go, Javascript and more

myria

Myria is a scalable Analytics-as-a-Service platform based on relational algebra.

notebooks

Various notebooks and tutorials on subjects of interest.

pomegranate

Fast, flexible and easy to use probabilistic modelling in Python.

pomegranate_archive

This is an archive of pomegranate 0.14.8 before the PyTorch remake for posterity.

pomegranate_wheel_builder

A temporary repository to play around with building wheels for the notoriously popular and industry revolutionizing package 'pomegranate'

py2neo

Py2neo is a simple and pragmatic Python library that provides access to the popular graph database Neo4j via its RESTful web service interface. With no external dependencies, installation is straightforward and getting started with coding is easy. The library is actively maintained on GitHub, regularly updated in the Python Package Index and is built uniquely for Neo4j in close association with its team and community.

pypore

Tools used to analyze data from nanopore-based experiments.

pystruct

Simple structured learning framework for python