Harms Lab @ University of Oregon

vertebrate-tlr4-evolution

scripts for reproducing vertebrate tlr4 synteny analysis

pdbtools

A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

phylogenetics

A Python API for managing phylogenetics projects

gpseer

A Python API that predicts missing data in sparsely sampled genotype-phenotype maps

gpmap

A Python API for managing genotype-phenotype map data

epistasis

A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.

phagedisplay

Analysis tools for phage display experiments in the Harms Lab

library_simulator

python package for simulating random libraries made by an error-prone polymerase

gpgraph

NetworkX for genotype-phenotype maps

pytc

python program for analyzing isothermal titration calorimetry data

genotype-phenotype-maps

A curated list of experimental genotype-phenotype maps from published literature in JSON format

bcmap

map barcodes to full sequences from a high-throughput mapping experiment

fast_dbscan

fast, lightweight dbscan implementation for peptide strings

gpvolve

A Python API for computing evolutionary paths across genotype-phenotype maps and clustering of genotype-phenotype maps.

latticegpm

Python package for building fitness landscapes from protein lattice models

pytc-gui

PyQt5 GUI for pytc API

reveal-presentation-template

html and basic directory structure template for (relatively) easily creating reveal.js slideshows

epistasis-notebooks

Tutorial notebooks for the epistasis package hosted on Binder.

hops

Use machine learning to find rules for peptide binding

latticeproteins

2d protein lattice model simulator in Python

wheeler-harms-S100A5-Ca-Cu-data

notebooks-epistasis-ensembles

Notebooks demonstrating the origins of high-order epistasis from statistical mechanical ensembles

notebooks-nonlinear-high-order-epistasis

Jupyter notebooks for Genetics paper, "Detecting high-order epistasis in nonlinear genotype-phenotype maps"

hops_enrich

software for processing phage display data for machine learning with peplearn

pytc-demos

Set of jupyter notebooks illustrating the pytc API.

pytc-binder

example jupyter notebooks demonstrating pytc fitting