networks-biology

There are 55 repositories under networks-biology topic.

  • pybel/pybel

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

    Language:Python131939432

  • saezlab/OmnipathR

    R client for the OmniPath web service

    Language:R112109820

  • covid19kg/covid19kg

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

    Language:Python45558

  • mikelkou/fava

    Functional Associations using Variational Autoencoders

    Language:Jupyter Notebook38153

  • pedroj/bipartite_plots

    `ggbipart`, an R package for plotting bipartite networks

    Language:HTML328617
  • doctoral-thesis

    cthoyt/doctoral-thesis

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

    Language:TeX29972

  • drug2ways/drug2ways

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

    Language:Python26587

  • bio2bel/kegg

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

    Language:Python135164

  • MuonRay/QuantumNetworkSimulations

    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 quantum many-body systems and networks made tractable using the quantum newtons cradle. A full showcase of this project is discussed in the following videos:https://www.youtube.com/watch?time_continue=115&v=WX3Ds_xCOaE

    Language:Python13202

  • PedroMTQ/UniFuncNet

    A multi-reference network annotation tool to support omics analysis

    Language:Python12100

  • yollct/spycone

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

    Language:Python12270

  • bel2scm/bel2scm

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

    Language:Jupyter Notebook101174

  • bio2bel/drugbank

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

    Language:Python9254

  • alextkalinka/linkcomm

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

    Language:R7112

  • daniaki/pyPPI

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

    Language:Python7315

  • PathwayMerger/PathMe-Viewer

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

    Language:JavaScript62173

  • bio2bel/hmdb

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

    Language:Python5381

  • bio2bel/reactome

    Integration of pathway-related information from Reactome in BEL

    Language:Python54151

  • montilab/ppi-context

    Contextualization of protein-protein interaction databases by cell line

    Language:Python5330

  • bel-commons/bel-commons

    An environment for curating, validating, and exploring knowledge assemblies encoded in BEL

    Language:HTML4111820

  • ELIFE-ASU/Neet

    Simulating and analyzing dynamical network models

    Language:Python4169410

  • marmello77/mello-et-al-2019-SD1

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

    Language:R4401

  • montilab/shine

    Structure Learning for Hierarchical Networks

    Language:R4402

  • pharmacome/conib

    Curation of Neurodegeneration in Biological Expression Language (CONIB)

    Language:Jupyter Notebook42127

  • hemekg/hemekg

    Modeling heme pathogenicity and pathway dysregulation in the context of hemolytic disorders

    Language:Python3413

  • bdpedigo/neuropull

    A (soon to be) lightweight Python package for accessing single-cell connectome networks with metadata.

    Language:Python2370

  • BioPhys-Turin/biophys-turin.github.io

    Official site of Biophys group at Unito

    Language:HTML2100

  • hooman650/BioModelChecker

    Bio-ModelChecker: Using Bounded Constraint Satisfaction to Seamlessly Integrate Observed Behavior with Prior Knowledge of Biological Networks

    Language:Python2312

  • bio2bel/bio2bel-manuscript

    LaTeX source for "Bio2BEL: Integration of Structured Knowledge with Biological Expression Language"

    Language:TeX121

  • bio2bel/go

    A Bio2BEL package for converting the Gene Ontology (GO) to BEL

    Language:Python125

  • DavisLaboratory/pyPPI

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

    Language:Python160

  • montilab/netviz

    A Shiny Application for Visualization and Analysis of Networks

    140

  • NeuroTechnologies/DyNetCP

    Codebase for discovery of latent dynamic connectivity in brain cortical networks

    Language:Jupyter Notebook1101

  • RobhooX/Robhoot

    Discovering sustainability in ecosystems

    Language:R1700

  • rwovenxkyears/ETH-Drain

    ETH Drain

    1100

  • saezlab/network_tools

    Collection of Python functions to run network-based analysis in signed and directed networks.

    Language:Jupyter Notebook1303