szhan Goto Github PK

3diphy

Maximum likelihood structural phylogenetics by including Foldseek 3Di characters. Supporting Information for Puente-Lelievre et al. 2023n for

allthebacteria

Follow up to Grace Blackwell's 661k dataset, for 2023

angiosperm-chromosome-number-evolution

Analysis of the rates of chromosome number evolution and lineage diversification in major angiosperm clades.

avocado_meets_ml

Yep, avocado meets machine learning.

bdendro

Bokeh helpers for visualizing a dendrogram.

bdmm-prime

Modified implementation of the BDMM multi-type birth-death model for BEAST 2.

bio_corex

A flexible version of CorEx developed for bio-data challenges that handles missing data, continuous/discrete variables, multi-CPU, overlapping structure, and includes visualizations

cherryml

Scalable Maximum Likelihood Estimation of Phylogenetic Models

coco

Numerical Black-Box Optimization Benchmarking Framework

cpp-recipes

Source code for 'C++ Recipes' by Bruce Sutherland

cssr-r

R interface to CSSR program, authored by https://github.com/stites/CSSR

ecdyn

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

factorial_hmm

FactorialHMM, a Python package for fast exact inference in Factorial Hidden Markov Models

game-on

Analysis of League of Legends game data

genomegamap

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

grapl

GRAPL: A computational library for nonparametric structural causal modelling, analysis and inference

hmmlearn

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

imodels

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

inst-spec

R scripts and data files to test the "instant speciation" hypothesis

lshmm

code to run Li and Stephens

memory

Analysis for CSSS2017 "memory" team

nltk

NLTK Source

numpy-100

100 numpy exercises (with solutions)

onekg_analysis

Evaluation of genotype imputation methods using the unified genealogy dataset

pagmo2

A C++ / Python platform to perform parallel computations of optimisation tasks (global and local) via the asynchronous generalized island model.

phylokit

Phylogenetics toolkit for the PyData Ecosystem

popgen-notes

Population genetics notes

probabilistic-programming-and-bayesian-methods-for-hackers

aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)

protein-sequence-models