jmschrei

pomegranate

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

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

yahmm

Yet Another Hidden Markov Model repository.

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.

tangermeme

Biological sequence analysis for the modern age.

torchegranate

A temporary repository hosting a pomegranate re-write using PyTorch as the backend.

ledidi

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

tfmodisco-lite

A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.

notebooks

Various notebooks and tutorials on subjects of interest.

bpnet-lite

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

rambutan

Prediction of the 3D structure of the genome through statistically significant Hi-C contacts.

dragonnfruit

A method for analyzing scATAC-seq experiments.

constraint_graphs

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

deep-learning-notes

Experiments with Deep Learning

hmmlearn

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

jmschrei.github.io

kiwano

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

lifelines

Survival analysis in Python

pystruct

Simple structured learning framework for python

blueberry

Inference of the 3D structure of genomes

COVID-19

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

kantalope

because it can't alope

keras

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

mxnet

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

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'

readthedocs.org

source code to readthedocs.org

sail-blog

The SAIL blog

shap

A unified approach to explain the output of any machine learning model.

xgboost

Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Flink and DataFlow