Performant, pure-Python subgraph isomorphism and monomorphism search (aka "motif search")

A Python package for gene network analysis

A Python toolkit for setting up benchmarking dataset using biomedical networks

Source code and data for "Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery"

NXOntology data: making ontologies accessible as simple JSON files

NHC: A computational approach to detect physiological homogeneity in the midst of genetic heterogeneity

A MUlti-species Network Kernel algorithm to embed proteins from a target network into a source network, creating cross-species representations for various comparative and predictive tasks

A Python package for network analysis through diffusion label propagation algorithms

A Python package for analyzing harmonized biological networks through diffusion algorithms

STRING protein network dataset downloads and transformations

Scripts and data from "Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms"

Simulating and analyzing dynamical network models

A knowledge graph of the wastewater treatment microbiome and its biological context

Simulation of interactions miRNA:Competing Targets

TBN_learning is a MATLAB implemented hybrid algorithm for learning the structure of transcriptional Bayesian networks on a genome-wide scale.

Code for my Master project

This repository contains companion codes, developed for use with the CRC Press Book "An Introduction to Systems Biology" by Karthik Raman

centrality measures in ecological networks

A web interface for ontology-based protein network visualization.

Semantic Capture of Relationships In Biological Literature (scribl)