Harms Lab @ University of Oregon (@harmslab)
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harmslab

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Top repositories

1

pdbtools

A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files
Python
162
star
2

epistasis

A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
Python
32
star
3

topiary

Python framework for doing ancestral sequence reconstruction
Python
27
star
4

pytc

python program for analyzing isothermal titration calorimetry data
Python
26
star
5

gpmap

A Python API for managing genotype-phenotype map data
Python
11
star
6

hops

Use machine learning to find rules for peptide binding
Jupyter Notebook
7
star
7

fast_dbscan

fast, lightweight dbscan implementation for peptide strings
C
6
star
8

phylogenetics

A Python API for managing phylogenetics projects
Python
6
star
9

notebooks-nonlinear-high-order-epistasis

Jupyter notebooks for Genetics paper, "Detecting high-order epistasis in nonlinear genotype-phenotype maps"
Jupyter Notebook
6
star
10

gpseer

A tool to predict missing data in sparsely sampled genotype-phenotype maps
Python
5
star
11

pytc-demos

Set of jupyter notebooks illustrating the pytc API.
Jupyter Notebook
3
star
12

examl-tree-ancestor

pipeline stitching together fasttree, examl, and lazarus/paml for phylogenetics and ancestral sequence reconstruction
Python
3
star
13

gpvolve

A Python API for computing evolutionary paths across genotype-phenotype maps and clustering of genotype-phenotype maps.
Python
3
star
14

dataprob

Library for fitting models using a likelihood framework.
Python
3
star
15

topiary-examples

Jupyter notebooks demonstrating the topiary ancestral sequence reconstruction package
Jupyter Notebook
2
star
16

TreeViewer

Interactive Evolutionary Tree Viewer using D3.js
JavaScript
2
star
17

pytc-gui

PyQt5 GUI for pytc API
Python
2
star
18

latticegpm

Python package for building fitness landscapes from protein lattice models
Python
2
star
19

genotype-phenotype-maps

A curated list of experimental genotype-phenotype maps from published literature in JSON format
Python
2
star
20

asr-protocol

Protocol and scripts for doing ancestral sequence reconstruction
Jupyter Notebook
1
star
21

flowsym

A Python API for simulating flow cytometry data.
Python
1
star
22

gpgraph

NetworkX for genotype-phenotype maps
Python
1
star
23

notebooks-epistasis-ensembles

Notebooks demonstrating the origins of high-order epistasis from statistical mechanical ensembles
Jupyter Notebook
1
star
24

phagedisplay

Analysis tools for phage display experiments in the Harms Lab
Python
1
star
25

latticeproteins

2d protein lattice model simulator in Python
Python
1
star