gene-regulatory-network

There are 8 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.
single-cell transcriptomics gene-regulatory-network transcription-factors
Language:Python 383
pinellolab / dictys
Context specific and dynamic gene regulatory network reconstruction and analysis
gene-regulatory-network network-analysis network-inference network-visualization single-cell-analysis single-cell-multiomics single-cell-network dynamic-network
Language:Python 99
netZoo / netZooR
netZooR is a network biology package implemented in R.
gene-regulatory-network transcription-factors
Language:R 93
netZoo / netZooPy
netZooPy is a network biology package implemented in Python.
gene-regulatory-network transcription-factors
Language:Jupyter Notebook 73
aertslab / SCope
Fast visualization tool for large-scale and high dimensional single-cell data
single-cell large-scale-data-visualization gene-expression gene-regulatory-network aws cloud loom reactjs grpc
Language:Python 68
netZoo / netbooks
Netbooks is a JupyterHub catalog of use cases in gene regulatory network inference using netZoo methods..
gene-regulatory-network transcription-factors
Language:Jupyter Notebook 39
SUwonglab / PECA
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
gene-regulatory-network gene-expression chromatin-accessibiity dnase-seq atac-seq rna-seq
Language:MATLAB 39
cailab-tamu / scTenifoldKnk
R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.
gene-knockout virtual-knockout-experiments gene-function functional-genomics gene-regulatory-network
Language:R 34
netZoo / netZooC
netZooC is a network biology package implemented in C.
gene-regulatory-network transcription-factors
Language:C 26
netZoo / netZooM
netZooM is a network biology package implemented in MATLAB.
gene-regulatory-network transcription-factors
Language:MATLAB 26
rvinas / adversarial-gene-expression
Adversarial generation of gene expression data using Generative Adversarial Networks
gan adversarial-networks adversarial-machine-learning bioinformatics gene-expression gene-regulatory-network machine-learning generative-adversarial-network e-coli keras tensorflow
Language:Jupyter Notebook 24
dpeerlab / scKINETICS
Code for scKINETICS (ISMB 2023)
atac-seq expectation-maximization gene-regulatory-network single-cell-analysis
Language:Jupyter Notebook 20
lingfeiwang / normalisr
Causal inference, differential expression, and co-expression for scRNA-seq
scrna-seq association-testing differential-expression co-expression normalization hypothesis-testing single-cell gene-regulatory-network single-cell-crispr-screening causal-inference
Language:Python 17
SUwonglab / rss-net
Regression with Summary Statistics exploiting Network Topology.
gwas-summary-statistics gene-regulatory-network bayesian-methods variational-inference gene-prioritization enrichment-analysis
Language:R 17
EngreitzLab / gene_network_evaluation
Evaluation framework for computationally inferred gene networks from single-cell data.
enhancer-prediction gene-co-expression-network gene-regulatory-network single-cell-genomics
Language:Python 7
Genome3d / psychiatric_and_cognitive_multimorbidities
Analysis of regulatory impacts of GWAS SNPs associated with psychiatric disorders and cognitive functioning.
schizophrenia depression hi-c psychiatric-disorders cognition adhd bipolar-disorder 3d-genome gene-regulatory-network anxiety multi-morbidity eqtl
Language:HTML 7
clreda / NORDic
Network-Oriented Repurposing of Drugs Python Package
bandit-algorithm boolean-network drug-repurposing gene-regulatory-network gene-regulatory-network-inference drug-simulation
Language:Jupyter Notebook 6
JChander / DeepRIG
A deep model infers gene regulation networks from scRNA-seq data.
deep-learning gene-regulatory-network graph-convolutional-network single-cell-rna-seq
Language:Jupyter Notebook 6
xichensf / magical
R and MATLAB scripts for MAGICAL
non-commercial-license bayesian-inference gene-regulatory-network single-cell-multiomics
Language:R 6
shuzwang / P2_cochlea
It contains the functional code to analyze P2 scRNA-seq and scATAC-seq data.
single-cell-omics gene-regulatory-network multiomics cochlea scrna-seq scatac-seq
Language:R 5
TuftsBCB / RegDiffusion
Diffusion model for gene regulatory network inference.
diffusion-models gene-regulatory-network grn single-cell
Language:Python 5
WWXkenmo / NetID_package
A scalable method to infer fate specific gene regulatory network from single cell gene expression data
cell-fate-determination gene-regulatory-network single-cell-rna-seq trajectory-analysis
Language:R 5
durenzn / PECA
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
gene-regulatory-network chromatin-accessibiity gene-expression dnase-seq atac-seq rna-seq
Language:MATLAB 4
bioPIDcontrol
mgschiavon / bioPIDcontrol
Code used for simulations & analysis in Chevalier, Gómez-Schiavon et al. (2019; Cell Systems)
control synthetic-biology modeling circuit gene-regulatory-network
Language:MATLAB 4
QuackenbushLab / grand
GRAND database of gene regulatory networks.
gene-regulatory-network
Language:JavaScript 4
evanamartin / baycn
A Metropolis-Hastings algorithm for inferring edge probabilities in a Bayesian network
r gene-regulatory-network directed-acyclic-graph
Language:R 3
Genome3d / alcohol-dependence
Analysis of tissue-specific regulatory impacts of alcohol dependence-associated SNPs.
alcohol-dependence gene-regulatory-network adh-genes hi-c 3d-genome eqtl
Language:HTML 3
JBris / nextflow-graph-machine-learning
A Nextflow pipeline demonstrating how to train graph neural networks for gene regulatory network reconstruction using DREAM5 data.
deep-learning graph-neural-network graph-neural-networks nextflow nextflow-pipeline nextflow-pipelines docker docker-compose gene-regulatory-network gene-regulatory-network-inference gene-regulatory-networks dream5 machine-learning minio mlflow mlops graphsage variational-autoencoder variational-inference
Language:Python 3
MihirBafna / clarify
Multi-level Graph Autoencoder (GAE) to clarify cell cell interactions and gene regulatory network inference from spatially resolved transcriptomics
cell-cell-interaction gene-regulatory-network graph-auto-encoder
Language:Jupyter Notebook 3
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
gene-regulatory-network rshinyapp
Language:R 2
biomedbigdata / DysRegNet_package
Inferring patient-specific regulatory alterations
rna-seq statistics transcriptomics bioinformatics gene-regulatory-network linear-models systems-biology
Language:Jupyter Notebook 2
DabinJeong / GRN_construction_with_kernelCCA
Condition-Specific Gene Regulatory Network construction
grn gene-expression-profile gene-regulatory-network kernel-cca snakemake time-series network-dynamics condition-specific
Language:Python 2
HilarieSit / hmdbn
Re-implementation of Hidden Markov induced Dynamic Bayesian Network for inferring Gene Regulatory Networks from Drosophila time-series microarray data
hidden-markov-model gene-regulatory-network computational-biology
Language:Python 2
lcrawlab / multio-viz
A platform for the interactive assessment of gene regulatory networks
bioinformatics gene-regulatory-network genetics genomics in-silico-perturbation
Language:R 2
natmurad / WGCNA
This repository contains a Script for WGCNA based on the Tutorial of WGCNA page
bioinformatics gene-regulatory-network wgcna
Language:HTML 2
NctuICLab / GREMA
GREMA: Modelling of emulated gene regulatory networks with confidence levels based on evolutionary intelligence to cope with the underdetermined problem
gene-regulatory-network dream-challenge underdetermined-problem genetic-algorithm
Language:C++ 2

gene-regulatory-network

aertslab / pySCENIC

pinellolab / dictys

netZoo / netZooR

netZoo / netZooPy

aertslab / SCope

netZoo / netbooks

SUwonglab / PECA

cailab-tamu / scTenifoldKnk

netZoo / netZooC

netZoo / netZooM

rvinas / adversarial-gene-expression

dpeerlab / scKINETICS

lingfeiwang / normalisr

SUwonglab / rss-net

EngreitzLab / gene_network_evaluation

Genome3d / psychiatric_and_cognitive_multimorbidities

clreda / NORDic

JChander / DeepRIG

xichensf / magical

shuzwang / P2_cochlea

TuftsBCB / RegDiffusion

WWXkenmo / NetID_package

durenzn / PECA

mgschiavon / bioPIDcontrol

QuackenbushLab / grand

evanamartin / baycn

Genome3d / alcohol-dependence

JBris / nextflow-graph-machine-learning

MihirBafna / clarify

arendma / GRN_web

biomedbigdata / DysRegNet_package

DabinJeong / GRN_construction_with_kernelCCA

HilarieSit / hmdbn

lcrawlab / multio-viz

natmurad / WGCNA

NctuICLab / GREMA