gene-regulatory-network

There are 63 repositories under gene-regulatory-network topic.

  • aertslab/pySCENIC

    pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

    Language:Python39618509176

  • pinellolab/dictys

    Context specific and dynamic gene regulatory network reconstruction and analysis

    Language:Python10134813

  • netZoo/netZooR

    netZooR is a network biology package implemented in R.

    Language:R9522739

  • netZoo/netZooPy

    netZooPy is a network biology package implemented in Python.

    Language:Jupyter Notebook7444232

  • aertslab/SCope

    Fast visualization tool for large-scale and high dimensional single-cell data

    Language:Python69934514

  • SUwonglab/PECA

    PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

    Language:MATLAB405146

  • netZoo/netbooks

    Netbooks is a JupyterHub catalog of use cases in gene regulatory network inference using netZoo methods..

    Language:Jupyter Notebook3942023

  • cailab-tamu/scTenifoldKnk

    R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.

    Language:R368255

  • netZoo/netZooC

    netZooC is a network biology package implemented in C.

    Language:C26204

  • netZoo/netZooM

    netZooM is a network biology package implemented in MATLAB.

    Language:MATLAB26217

  • rvinas/adversarial-gene-expression

    Adversarial generation of gene expression data using Generative Adversarial Networks

    Language:Jupyter Notebook24325

  • dpeerlab/scKINETICS

    Code for scKINETICS (ISMB 2023)

    Language:Jupyter Notebook20243

  • lingfeiwang/normalisr

    Causal inference, differential expression, and co-expression for scRNA-seq

    Language:Python17213

  • SUwonglab/rss-net

    Regression with Summary Statistics exploiting Network Topology.

    Language:R17404

  • EngreitzLab/gene_network_evaluation

    Evaluation framework for computationally inferred gene networks from single-cell data.

    Language:Jupyter Notebook8306

  • Genome3d/psychiatric_and_cognitive_multimorbidities

    Analysis of regulatory impacts of GWAS SNPs associated with psychiatric disorders and cognitive functioning.

    Language:HTML8703

  • JChander/DeepRIG

    A deep model infers gene regulation networks from scRNA-seq data.

    Language:Jupyter Notebook8211

  • xichensf/magical

    R and MATLAB scripts for MAGICAL

    Language:R7101

  • clreda/NORDic

    Network-Oriented Repurposing of Drugs Python Package

    Language:Jupyter Notebook6201

  • shuzwang/P2_cochlea

    It contains the functional code to analyze P2 scRNA-seq and scATAC-seq data.

    Language:R5200

  • TuftsBCB/RegDiffusion

    Diffusion model for gene regulatory network inference.

    Language:Python51901

  • WWXkenmo/NetID_package

    A scalable method to infer fate specific gene regulatory network from single cell gene expression data

    Language:R5111

  • durenzn/PECA

    PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

    Language:MATLAB4120
  • bioPIDcontrol

    mgschiavon/bioPIDcontrol

    Code used for simulations & analysis in Chevalier, Gómez-Schiavon et al. (2019; Cell Systems)

    Language:MATLAB4202

  • MihirBafna/clarify

    Multi-level Graph Autoencoder (GAE) to clarify cell cell interactions and gene regulatory network inference from spatially resolved transcriptomics

    Language:Jupyter Notebook4300

  • QuackenbushLab/grand

    GRAND database of gene regulatory networks.

    Language:JavaScript4572

  • evanamartin/baycn

    A Metropolis-Hastings algorithm for inferring edge probabilities in a Bayesian network

    Language:R3201

  • Genome3d/alcohol-dependence

    Analysis of tissue-specific regulatory impacts of alcohol dependence-associated SNPs.

    Language:HTML3702

  • JBris/nextflow-graph-machine-learning

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

    Language:Python3301

  • natmurad/WGCNA

    This repository contains a Script for WGCNA based on the Tutorial of WGCNA page

    Language:HTML3100

  • arendma/GRN_web

    This repository contains the source code for the R Shiny server application allowing to query the gene regulatory network presented in https://www.nature.com/articles/s41467-023-38183-4

    Language:R22170

  • DabinJeong/GRN_construction_with_kernelCCA

    Condition-Specific Gene Regulatory Network construction

    Language:Python2101

  • daisybio/DysRegNet_package

    Inferring patient-specific regulatory alterations

    Language:Jupyter Notebook220

  • HilarieSit/hmdbn

    Re-implementation of Hidden Markov induced Dynamic Bayesian Network for inferring Gene Regulatory Networks from Drosophila time-series microarray data

    Language:Python2100

  • lcrawlab/multio-viz

    A platform for the interactive assessment of gene regulatory networks

    Language:R2200

  • NctuICLab/GREMA

    GREMA: Modelling of emulated gene regulatory networks with confidence levels based on evolutionary intelligence to cope with the underdetermined problem

    Language:C++2201