🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

• UpdatedJun 26, 2024
• Python

R client for the OmniPath web service

• UpdatedFeb 25, 2025
• R

COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology

• UpdatedJul 5, 2021
• Python

Functional Associations using Variational Autoencoders

• UpdatedFeb 4, 2025
• Jupyter Notebook

`ggbipart`, an R package for plotting bipartite networks

• UpdatedFeb 12, 2025
• HTML

📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology

• UpdatedDec 16, 2019
• TeX

A Python package for drug discovery by analyzing causal paths on multiscale networks

• UpdatedJul 1, 2024
• Python

A series of simulation codes used to emulate quantum-like networks in the simulation of emergent adaptive behavior, such as network synchronization, and relate the nature of the coupled harmonic oscillators with non-local behavior and chimera states in systems of quantum particles. Coding Used is based on mathematical modelling of transport in q…

• UpdatedAug 8, 2024
• Python

A Bio2BEL package for integrating pathway-related information from KEGG in BEL

• UpdatedFeb 11, 2022
• Python

A multi-reference network annotation tool to support omics analysis

• UpdatedMay 31, 2022
• Python

Splicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data

• UpdatedJun 29, 2024
• Python

Generate dynamic structural causal models from biological knowledge graphs encoded in the Biological Expression Language (BEL)

• UpdatedJan 11, 2021
• Jupyter Notebook

A Bio2BEL package for DrugBank (https://www.drugbank.ca)

• UpdatedDec 14, 2020
• Python

A machine learning tool to assign edges in protein-protein interaction networks with a function.

• UpdatedFeb 13, 2020
• Python

Tools for Generating, Visualising, and Analysing Link Communities in Networks

• UpdatedFeb 4, 2021
• R

A Bio2BEL package for converting the Human Metabolite Database (HMDB) to BEL

• UpdatedApr 29, 2019
• Python

A web application for visualizing and exploring pathway knowledge in Biological Expression Language (BEL)

• UpdatedJan 9, 2020
• JavaScript

Structure Learning for Hierarchical Networks

• UpdatedMay 18, 2021
• R

Contextualization of protein-protein interaction databases by cell line

• UpdatedMar 3, 2021
• Python

Supplementary data 1 of the paper Mello et al. 2019 (NatureEcoEvo).

• UpdatedOct 19, 2021
• R