This repository contains code and datasets related to entity/knowledge papers from the VERT (Versatile Entity Recognition & disambiguation Toolkit) project, by the Knowledge Computing group at Microsoft Research Asia (MSRA).

• UpdatedMar 16, 2024
• Python

Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples.

• UpdatedMar 6, 2024
• Python

scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference

• UpdatedSep 20, 2024
• R

Diffusion model for gene regulatory network inference.

• UpdatedMar 16, 2025
• Python

a novel method of gene regulatory network structure inference

• UpdatedNov 6, 2020
• MATLAB

Official Implementation of Context-Dependent Gene Regulatory Networks (CDGRNs)

• UpdatedFeb 20, 2023
• Julia

SCANet is a python package that incorporates the inference of gene co-expression networks from single-cell gene expression data

• UpdatedMar 23, 2023
• Python

This package implements a benchmarking of several gene network inference algorithms from gene expression data

• UpdatedMay 17, 2020
• R

This is a repository for creating a UAV network based on the GRN graph using python.

• UpdatedApr 9, 2024
• Python

Condition-Specific Gene Regulatory Network construction

• UpdatedDec 1, 2021
• Python

An experiment to tag ner entities related with biological molecular species using spaCy, fine-tuning a spacy's pipeline, and building a knowledge base of regulatory events, in order to model a gene regulatory network from them.

• UpdatedFeb 4, 2025
• Prolog

This repository provides a model of the MAPK and Akt pathways. Parameters and initial values are mainly based on biological assumptions. The model is therefore conceptual, and the purpose is to get a better understanding of the interactions between genes, that are important in some cancers.

• UpdatedDec 17, 2024
• R

Novel statistical methodology for FDR(False Discovery Rate) analysis of Gene Regulatory Networks

• UpdatedJan 26, 2025
• Python

biopatternsg is a system that builds gene regulatory networks from a basic collection of biological objects, gathering and processing PubMed abstracts, using Internet available informational resources like Mesh, GeneOntology, UniProt, PDB and others, and that uses java and logical engines like prolog to integrate and analyse them.

• UpdatedFeb 16, 2025

An experiment to tag ner entities related with biological molecular species using spaCy, fine-tuning a spacy's pipeline, and building a knowledge base of regulatory events, in order to model a gene regulatory network.

• UpdatedFeb 27, 2023
• Prolog

python version of NestBoot-FDR

• UpdatedMar 17, 2025
• Python

A tool for visualizing gene regulatory networks

• UpdatedMar 19, 2025
• Python

CUDA code for DE+PSO for Gene Regulatory Network inference

• UpdatedSep 6, 2023
• Cuda

Rodrigo García-Valiente, Elena Merino, Antoine van Kampen. ABM of the germinal center with implementation of SHM fate tree, sequence representation and PC/MBC gene network.

• UpdatedJul 20, 2022
• Standard ML

Inferring GRN from scRNA-seq data.

• UpdatedOct 5, 2022
• R