sysbiolab/PathwaySpace

PathwaySpace is an R package that creates landscape images from graphs containing vertices (nodes), edges (lines), and a signal associated with the vertices.

Language: R - Size: 9.42 MB - Last synced: about 3 hours ago - Pushed: about 20 hours ago - Stars: 1 - Forks: 0

krishnanlab/PyGenePlexus

A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input gene list.

Language: Python - Size: 4.44 MB - Last synced: 3 days ago - Pushed: 8 days ago - Stars: 19 - Forks: 3

alyst/HierarchicalHotNet.jl

Julia implementation of Hierarchical HotNet method

Language: Julia - Size: 656 KB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 2 - Forks: 0

colomoto/colomoto-docker

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Language: Jupyter Notebook - Size: 9.1 MB - Last synced: about 4 hours ago - Pushed: about 5 hours ago - Stars: 24 - Forks: 9

drugst-one/plugin

Drugst.One is a plug-and-play solution to make your biomedical (web-)tool drug repurposing ready. With just three lines of code the plugin can be integrated into your website within a few minues of work.

Language: HTML - Size: 8.52 MB - Last synced: 20 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 1

cantinilab/HuMMuS

Molecular interactions inference from single-cell multi-omics data

Language: Python - Size: 78.4 MB - Last synced: 23 days ago - Pushed: 24 days ago - Stars: 13 - Forks: 3

emosca-cnr/mND

mND uses multi-layer Network Diffusion to find gene networks that contain high scoring genes. It considers two or more "layers" of genome-wide scores and an interactome.

Language: R - Size: 26.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

mims-harvard/life-tree

Evolution of protein interactomes across the tree of life

Language: C++ - Size: 14.6 KB - Last synced: about 2 months ago - Pushed: over 4 years ago - Stars: 8 - Forks: 5

enggiqbal/Webinar-NetworkAnalysis

Webinar: Large-scale Biological Network Analysis and Visualization Using CyVerse

Language: Python - Size: 18.3 MB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

AstraZeneca/onto_merger

OntoMerger is an ontology alignment library for deduplicating knowledge graph nodes that represent the same domain.

Language: HTML - Size: 32.8 MB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 90 - Forks: 5

ptgm/bioNuSMV Fork of hklarner/NuSMV-a

bioNuSMV is a fork and extension of https://github.com/hklarner/NuSMV-a, which adds a handful of features to ease the use of model checking by biological modelers, in particular, in the context of the verification of qualitative regulatory networks

Language: C - Size: 12 MB - Last synced: 2 months ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 1

ladyson1806/SerohijosLab-piQTL

GitHub Repository associated with the piQTL project (Mapping effects of genome-wide genetic variation to protein-protein interactions reveals molecular mechanisms of complex traits) [ Serohijos & Michnick Lab, Université de Montréal ]

Language: Jupyter Notebook - Size: 1.72 GB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 4 - Forks: 1

dvklopfenstein/ReactomePy

Explore biomolecular pathways in Reactome from the command-line or a Python script

Language: Python - Size: 17.3 MB - Last synced: 15 days ago - Pushed: 6 months ago - Stars: 21 - Forks: 4

Axelwickm/NeuroCorrelation

3D Spiking neural network simulation exploring Spike Timing Dependent Plasticity (STDP)

Language: C++ - Size: 1.63 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 5 - Forks: 1

arnaudporet/pathrider

Finding paths of interest in networks

Language: Go - Size: 2.3 MB - Last synced: 4 months ago - Pushed: about 2 years ago - Stars: 3 - Forks: 2

krashkov/SteinerNet

R Package: Steiner tree approach for graph analysis

Language: R - Size: 1.03 MB - Last synced: 4 months ago - Pushed: 12 months ago - Stars: 8 - Forks: 5

PathwayAnalysisPlatform/PathwayMatcher_Dev 📦

PathwayMatcher is a free, open-source software to search for pathways related to a list of proteins in Reactome. This repository is the development repository. For the latest version see: https://github.com/PathwayAnalysisPlatform/PathwayMatcher

Language: Java - Size: 1.72 GB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 6 - Forks: 1

LSI-UniKonstanz/vanted

Visualisation and Analysis of Networks conTaining Experimental Data

Language: Java - Size: 240 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 7 - Forks: 0

emosca-cnr/dmfind002

Network diffusion-based analysis of omics for the identifcation of differentially enriched modules.

Language: R - Size: 251 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

kckishan/BioNetEmbedding

PyTorch Implementation of Biological Network Embedding.

Language: Jupyter Notebook - Size: 1.22 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 3 - Forks: 0

bradduthie/RandomMatrixStability

R package associated with paper "Component response rate variation underlies the stability of highly complex finite systems" (Duthie, AB. 2020. Sci. Rep. 10:8296, https://www.nature.com/articles/s41598-020-64401-w). This repository contains all manuscript text and supplemental information, and all code for recreating analyses.

Language: HTML - Size: 253 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

tripal/tripal_network

Provides Tripal integration of biological networks including storage, loaders and visualzations

Language: PHP - Size: 4.51 MB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 1 - Forks: 0

arnaudporet/stream 📦

Streaming over networks

Language: Go - Size: 78.1 KB - Last synced: 9 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

arnaudporet/sbgn2sif

Converting SBGN encoded pathways to the SIF file format

Language: Python - Size: 185 KB - Last synced: 9 months ago - Pushed: about 4 years ago - Stars: 2 - Forks: 2

arnaudporet/konect 📦

Connecting nodes

Language: Go - Size: 259 KB - Last synced: 9 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

arnaudporet/kgml2sif

Converting KGML encoded KEGG pathways to the SIF file format

Language: Python - Size: 2.96 MB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 2

sbgn/cd2sbgnml Fork of royludo/cd2sbgnml

Translation between CellDesigner-flavoured SBML and SBGN-ML

Language: Java - Size: 21.1 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 6 - Forks: 2

arnaudporet/kali

In silico therapeutic target discovery using network attractors: avoiding pathological phenotypes

Language: Go - Size: 982 KB - Last synced: 9 months ago - Pushed: about 2 years ago - Stars: 5 - Forks: 0

drugst-one/backend

This is the backend service repository that makes Drugst.One work. Drugst.One is a plug-and-play solution to make your biomedical (web-)tool drug repurposing ready. With just three lines of code the plugin can be integrated into your website within a few minues of work.

Language: Python - Size: 19.7 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 0 - Forks: 1

Asplund-Samuelsson/POPPY

Prospecting Optimal Pathways with PYthon: Tools for creating and exploring metabolic reaction networks.

Language: Python - Size: 37 MB - Last synced: 10 months ago - Pushed: over 2 years ago - Stars: 2 - Forks: 1

biomedbigdata/keypathwayminer-R

R package for de novo pathway enrichment using KeyPathwayMiner

Language: R - Size: 39.9 MB - Last synced: 30 days ago - Pushed: 11 months ago - Stars: 4 - Forks: 1

seyuboglu/milieu

Mutual Interactors: A graph-based machine learning model with applications in molecular phenotype prediction

Language: Jupyter Notebook - Size: 177 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 6 - Forks: 1

raminmh/Worm-Blogging

Here, I include my thoughts about how does the brain of the worm give rise to remarkable behavioral plasticities

Size: 6.84 KB - Last synced: 4 months ago - Pushed: over 6 years ago - Stars: 2 - Forks: 1

basiralab/MGN-Net

MGN-Net: A novel Graph Neural Network for integrating heterogenous graph population derived from multiple sources.

Language: Python - Size: 6.63 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 6 - Forks: 4

wangboyunze/Network_Enhancement

Language: Matlab - Size: 10.6 MB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 27 - Forks: 11

huidr/spectral-graph-analysis

Using spectral graph theory to analyze two biological networks

Language: TeX - Size: 3.13 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

pietrocinaglia/dante

DANTE is a software tool able to align two dynamic networks. It bases its computation on the temporal embeddings.

Size: 296 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

MichaelBatskinis95/Graph-DB-4-Hematological-Data

Cypher Queries regarding Hematological Markers Network Markers DB in Neo4j

Language: Jupyter Notebook - Size: 243 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

abduallahmohamed/MCRM

MCRM: Mother Compact Recurrent Memory

Language: Python - Size: 14.6 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 5 - Forks: 0

bhklab/CrosstalkNet

A web resource to analyze bi-partite and non-bipartite biological networks.

Language: JavaScript - Size: 217 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 2 - Forks: 4

Dinh-SM/Mini-Project-MOGAMUN

Translation of the MOGAMUN algorithm in Python as part of a biological network modeling course.

Language: Python - Size: 189 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

anilozdemir/Bee-DCD

Repo for Bees outperform vertebrates in a delayed conditional learning task

Language: Jupyter Notebook - Size: 221 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

draeger-lab/SBMLsqueezer

Context-sensitive creation of kinetic equations in biochemical networks

Language: HTML - Size: 608 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 3 - Forks: 0

calugo/RNA-NETS

THREE.JS GENETIC CODE NEUTRAL NETWORK EXPLORER

Language: Jupyter Notebook - Size: 5.31 MB - Last synced: 29 days ago - Pushed: about 7 years ago - Stars: 1 - Forks: 1

MRIO/oliveML

neuroML models for reconstructed inferior olivary cells.

Language: MATLAB - Size: 7.14 MB - Last synced: 11 months ago - Pushed: over 4 years ago - Stars: 2 - Forks: 2

cannin/sbgn2sif Fork of arnaudporet/sbgn2sif

Converting SBGN-encoded pathways to the SIF file format

Language: Python - Size: 187 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 2 - Forks: 1

royludo/cd2sbgnml

Translation between CellDesigner-flavoured SBML and SBGN-ML

Language: Java - Size: 13.4 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 4 - Forks: 6

sankarshan-bhat/graph-clustering

This repository provides classic clustering algorithms and various internal cluster quality validation metrics and also visualization capabilities to analyse the clustering results

Language: Python - Size: 2.69 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

nsarang/motif_bionet

Identifying frequent patterns in graphs

Language: C++ - Size: 1.77 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

arnaudporet/smoosim

Enhancing Boolean networks with continuous logical operators and edge tuning: smoothing simulations

Language: R - Size: 84 KB - Last synced: 4 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 3

jtimonen/ode_mcmc

Probabilistic ODE model structure inference using MCMC

Language: Matlab - Size: 6.74 MB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0