Le Yuan's repositories
2018-ncbi-lineages
Extract lineage CSVs from NCBI for use with sourmash lca.
BayesianGEM
This repository contains code and data needed to replicate the analysis carried out in the manuscript Li G, et al. 2020.
rxn4chemistry
Python wrapper for the IBM RXN for Chemistry API
findPC
findPC: Automatic selection of number of principal components
HGTphyloDetect
HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.
Human-GEM
The generic genome-scale metabolic model of Homo sapiens
InterpretableMLBook
《可解释的机器学习--黑盒模型可解释性理解指南》，该书为《Interpretable Machine Learning》中文版
lihang-code
《统计学习方法》的代码实现
MammalianSecretoryRecon
Secretory Pathway Reconstruction for Human, CHO, and Mouse
molecularGNN_smiles
The code of a graph neural network (GNN) for molecules, which is based on learning representations of r-radius subgraphs (i.e., fingerprints) in molecules.
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
ncbitax2lin
🐞 Convert NCBI taxonomy dump into lineages
PecanPy
A fast, parallelized, memory efficient, and cache-optimized Python implementation of node2vec
public_scripts
collection of bioinformatic scripts
pytfa
A Python 3 implementation of Thermodynamics-based Flux Analysis
Python_course_2021
This is a repository for the course Python programming in 2021
Tome
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
tomerdesign
Improving enzyme optimum temperature prediction with resampling strategies and ensemble learning
UniRep-analysis
Analysis and figure code from Alley et al. 2019.