szhan

transformers

🤗 Transformers: State-of-the-art Machine Learning for Pytorch, TensorFlow, and JAX.

genealogy_workshop

genomics-research

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

ksw2

Global alignment and alignment extension

msprime

Simulate genealogical trees and genomic sequence data using population genetic models

tsdate

Infer the age of ancestral nodes in a tree sequence.

tutorials

A set of tutorials for msprime and tskit.

miceforest

Multiple Imputation with LightGBM in Python

imodels-data

Preprocessed data for various popular tabular datasets to go along with imodels.

imodels

Interpretable ML package 🔍 for concise, transparent, and accurate predictive modeling (sklearn-compatible).

tskit

Population-scale genomics

snipit

snipit: summarise snps relative to your reference sequence

pangolin

Software package for assigning SARS-CoV-2 genome sequences to global lineages.

lecture_notes

Lecture Notes on Computational and Mathematical Population Genetics

opencv

Open Source Computer Vision Library

imutils

A series of convenience functions to make basic image processing operations such as translation, rotation, resizing, skeletonization, and displaying Matplotlib images easier with OpenCV and Python.

FastaParser

A Python FASTA file Parser and Writer.

genomegaMap

Within-species genome-wide dN/dS estimation from very many genomes

dl-workshop

Crash course to master gradient-based machine learning. Also secretly a JAX course in disguise!

bayesian-stats-modelling-tutorial

How to do Bayesian statistical modelling using numpy and PyMC3

covidcg

A COVID-19 CoV Genetics (CG) browser to inform therapeutics development

serratus

Ultra-deep search for novel viruses

revbayes

Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

interpret

Fit interpretable models. Explain blackbox machine learning.

julia

The Julia Programming Language

rfishbase

R interface to the fishbase.org database

DendroPy

A Python library for phylogenetic scripting, simulation, data processing and manipulation.

scrappie

Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group

awesome-self-supervised-learning

A curated list of awesome self-supervised methods