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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

cameo

cameo - computer aided metabolic engineering & optimization

carveme_paper

Data and scripts for the paper "Fast automated reconstruction of genome-scale metabolic models for microbial species and communities"

cobrame

COBRA Toolbox for genome-scale models of metabolism and expression (ME-models)

cobrapy

COBRApy is a package for constraint-based modeling of biological networks

cpi_prediction

This is a code for compound-protein interaction (CPI) prediction based on a graph neural network (GNN) for compounds and a convolutional neural network (CNN) for proteins.

crispr_mismatch_analysis

d2l-zh

《动手学深度学习》：面向中文读者、能运行、可讨论。英文版即伯克利“深度学习导论”教材。

deepconv-dti

deepexpression

dleps

A Deep Learning based Efficacy Prediction System for drug discovery

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

metachip

Horizontal gene transfer (HGT) identification pipeline

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.

multiomicmechanismawareml

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

proteingan

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

rxn4chemistry

Python wrapper for the IBM RXN for Chemistry API