Pinned 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.
Biopython-cn
Biopython Tutorial Chinese Translation
ProteinGAN
rxn4chemistry
Python wrapper for the IBM RXN for Chemistry API
DLKcat
Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction
HGTphyloDetect
HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.
MLEssential
A computational toolbox to predict essential genes using machine learning based on sequence and evolution-based information
Multi_scale_evolution
Multi-scale evolution analysis of with aid of protein 3D structures for 332 different yeast species plus 11 fungal species.
Yeast-Species-GEMs
A universal metabolic model knowledge database (pan-GEM) for current existing yeast species with genome sequence, based on which we will build the GEMs of high quality for each yeast species.
le-yuan's Repositories
le-yuan/ProteinGAN
le-yuan/2018-ncbi-lineages
Extract lineage CSVs from NCBI for use with sourmash lca.
le-yuan/BayesianGEM
This repository contains code and data needed to replicate the analysis carried out in the manuscript Li G, et al. 2020.
le-yuan/cameo
cameo - computer aided metabolic engineering & optimization
le-yuan/rxn4chemistry
Python wrapper for the IBM RXN for Chemistry API
le-yuan/CRISPR_mismatch_analysis
le-yuan/DeepConv-DTI
le-yuan/DeepExpression
le-yuan/DLEPS
A Deep Learning based Efficacy Prediction System for drug discovery
le-yuan/findPC
findPC: Automatic selection of number of principal components
le-yuan/HGTphyloDetect
HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.
le-yuan/Human-GEM
The generic genome-scale metabolic model of Homo sapiens
le-yuan/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
le-yuan/lihang-code
《统计学习方法》的代码实现
le-yuan/MammalianSecretoryRecon
Secretory Pathway Reconstruction for Human, CHO, and Mouse
le-yuan/MetaCHIP
Horizontal gene transfer (HGT) identification pipeline
le-yuan/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.
le-yuan/multiOmicMechanismAwareML
le-yuan/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
le-yuan/ncbitax2lin
🐞 Convert NCBI taxonomy dump into lineages
le-yuan/PecanPy
A fast, parallelized, memory efficient, and cache-optimized Python implementation of node2vec
le-yuan/public_scripts
collection of bioinformatic scripts
le-yuan/pytfa
A Python 3 implementation of Thermodynamics-based Flux Analysis
le-yuan/Python_course_2021
This is a repository for the course Python programming in 2021
le-yuan/ssbio
A Python framework for structural systems biology
le-yuan/Tome
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
le-yuan/tomerdesign
Improving enzyme optimum temperature prediction with resampling strategies and ensemble learning
le-yuan/UniRep
UniRep model, usage, and examples.
le-yuan/UniRep-analysis
Analysis and figure code from Alley et al. 2019.
le-yuan/yuanle.github.io