Pinned Repositories
cobrapy
COBRApy is a package for constraint-based modeling of biological networks
DeepEnzyme
fastgraphGEM
R package for building and visualising GEM graphs automatically with aid of cellDesigner 4.4
hongPy
hongR
It is a R package to collect some easy codes for handy use
machine-learning-books
this is a fork of collection of books for machine learning.
Tutorial_for_Yeastspot3D
Tutorial for Yeastspot3D
Unified_Yeast_GEMs_Database
vivarium
a multi-scale simulation platform for whole-cell modeling
yeast-model-update
Data and code for yeast-GEM update
hongzhonglu's Repositories
hongzhonglu/hongR
It is a R package to collect some easy codes for handy use
hongzhonglu/Tutorial_for_Yeastspot3D
Tutorial for Yeastspot3D
hongzhonglu/AGORA
The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gut microbes through the use of issues. Please note that pull requests will be automatically closed.
hongzhonglu/atlas
ATLAS - Three commands to start analysing your metagenome data
hongzhonglu/Candida-albicans-microbiome-interaction
hongzhonglu/CarveFungi
hongzhonglu/datasets
NCBI Datasets is an experimental resource for finding and building datasets
hongzhonglu/deeplearning-models
A collection of various deep learning architectures, models, and tips
hongzhonglu/esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
hongzhonglu/genomics
Sphinx documentation source for a computational genomics tutorial.
hongzhonglu/KM_prediction
hongzhonglu/meneco
:m: Metabolic network completion
hongzhonglu/metaGEM
A Snakemake pipeline for the generation of MAGs, reconstruction of GEMs, and simulation of cross-feeding interactions within microbial communities from lab cultures, human gut, ocean, plant-associated, and bulk soil microbiomes
hongzhonglu/MetagenomeCourse2019
Course material for the metagenomics course
hongzhonglu/micom
Python package to study microbial communities using metabolic modeling.
hongzhonglu/MicrobiomeStatPlot
Interpretation and visualization of microbiome charts
hongzhonglu/MIGRENE
the toolbox for Microbial and personalized GEM, REactiobiome and community NEtwork modelling
hongzhonglu/ML-From-Scratch
Machine Learning From Scratch. Bare bones NumPy implementations of machine learning models and algorithms with a focus on accessibility. Aims to cover everything from linear regression to deep learning.
hongzhonglu/nglview
Jupyter widget to interactively view molecular structures and trajectories
hongzhonglu/Prochlorococcus_Model
Materials for Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus paper
hongzhonglu/PythonAlgorithms
All Algorithms implemented in Python 3
hongzhonglu/pytorchTutorial
PyTorch Tutorials from my YouTube channel
hongzhonglu/qiime2
Official repository for the QIIME 2 framework.
hongzhonglu/RaptorX-3DModeling
hongzhonglu/rp2paths
RetroPath2.0 to pathways
hongzhonglu/STAAR
An R package for performing STAAR procedure in whole genome sequencing studies
hongzhonglu/tellurium
Python Environment for Modeling and Simulating Biological Systems
hongzhonglu/transcriptutorial
This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
hongzhonglu/Yeastspot3D
The package is used to conduct the mutation cluster analysis with aid of protein 3D structures for yeast.
hongzhonglu/zga
ZGA prokaryotic genome assembly and annotation pipeline