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

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

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

centrality measures in ecological networks

A web interface for ontology-based protein network visualization.

Semantic Capture of Relationships In Biological Literature (scribl)