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gene-regulatory-network-inference

Here are 11 public repositories matching this topic...

clreda / NORDic

Network-Oriented Repurposing of Drugs Python Package

drug-repurposing boolean-network bandit-algorithm gene-regulatory-network gene-regulatory-network-inference drug-simulation

Updated Apr 23, 2025
Jupyter Notebook

calebclayreagor / DELAY

Depicting pseudotime-lagged causality for accurate gene-regulatory inference

deep-learning gene-regulation single-cell multi-omics gene-regulatory-networks gene-regulatory-network-inference

Updated Mar 25, 2025
Python

pdmoerland / SingleCellNotes

Links to interesting courses, tutorials, papers, software etc. related to single-cell omics data analysis

single-cell spatial-transcriptomics trajectory-inference cell-cell-interaction pseudotime-estimation gene-regulatory-network-inference

Updated May 26, 2024

JBris / nextflow-graph-machine-learning

A Nextflow pipeline demonstrating how to train graph neural networks for gene regulatory network reconstruction using DREAM5 data.

docker machine-learning deep-learning nextflow docker-compose minio variational-inference variational-autoencoder gene-regulatory-network graphsage graph-neural-networks mlops mlflow graph-neural-network nextflow-pipeline nextflow-pipelines gene-regulatory-networks gene-regulatory-network-inference dream5

Updated Nov 20, 2024
Python

SaniyaKhullar / NetREm

Network Regression Embeddings reveal cell-type Transcription Factor coordination for target gene (TG) regulation

transcription-factors protein-interaction network-regularization gene-expression-profiles transcriptional-regulatory-network single-cell-analysis ppi-networks network-lasso multiomics-data gene-regulatory-network-inference bioinformatics-software transcription-factor-coordination regularization-embeddings regression-embeddings predictor-interactions network-guided-regression regression-with-prior-knowledge network-based-inference netrem

Updated May 18, 2024
Jupyter Notebook

viktormiok / PhD-thesis

Latex scripts to compile my PhD thesis

rna-seq microarray splines ridge-regression multivariate-timeseries cervical-cancer gene-regulatory-network-inference

Updated Mar 11, 2025
TeX

JBris / dream5_grn_data

Gold standard gene regulatory network data from the DREAM5 challenge.

genomics network gene-network-inference gene-network gene-regulatory-network gene-network-reconstruction gene-regulatory-network-inference

Updated Jun 19, 2022

climatechangemicrobiology / ProGRN

Prokaryote Gene Regulatory Network (ProGRN) Inference Pipeline

machine-learning gene random-forest gene-expression microbiology bacteria transcriptomics regulatory-network methane multi-omics gene-regulatory-network methanotrophy genie3 regulatory-genomics gene-regulatory-network-inference aracne-network methylotroph methylomonas

Updated Apr 4, 2025
HTML

vksriharsha / Causal-Inference-on-Gene-Expression-Data

Python implementation of the PCA-CMI algorithm proposed by Zhang et al. and comparison of the results with the IC algorithm to predict gene regulatory network skeleton and edge orientations.

python machine-learning bioinformatics causal-inference gene-regulatory-network-inference

Updated Jun 28, 2022
Jupyter Notebook

AntoinePassemiers / PORTIA

A Lightning-fast algorithm for Gene Regulatory Network inference from gene expression data

gaussian-graphical-models end-to-end-machine-learning power-transforms gene-regulatory-network-inference

Updated Mar 20, 2023
Python

Stfort52 / NOLAN

TENET refined

single-cell transfer-entropy single-cell-rna-seq gene-regulatory-network pseudotime gene-regulatory-network-inference

Updated Feb 23, 2023
Python

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