gene-regulatory-networks

There are 3 repositories under gene-regulatory-networks topic.

graphein
a-r-j / graphein
Protein Graph Library
bioinformatics computational-biology deep-learning dgl drug-discovery gene-regulatory-networks geometric-deep-learning graph-neural-networks interactome interactomics ppi-networks protein protein-data-bank protein-design protein-structure python pytorch pytorch-geometric rna structural-biology
Language:Jupyter Notebook 989
liulab-dfci / MAESTRO
Single-cell Transcriptome and Regulome Analysis Pipeline
scatac-seq scrna-seq epigenetics snakemake-workflows transcription-factors gene-regulatory-networks
Language:C 263
graphsim
TomKellyGenetics / graphsim
R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)
r-stats igraph-networks simulated-data graph-algorithms package joss genetics gene-expression gene-regulatory-networks benchmarking simulation-modeling genomics genomic-data-analysis ngs-analysis
Language:R 22
cailab-tamu / scTenifoldNet
A R/MATLAB package to construct and compare gene regulatory networks from single-cell transcriptomic data
differential-regulation-analysis gene-regulatory-networks manifold-alignment single-cell tensor-decomposition
Language:R 19
ashleymaeconard / TIMEOR
TIMEOR: Trajectory Inference and Mechanism Exploration with Omics Data in R
transcription-factor time-series gene-regulatory-networks website r rshinyapp multi-omics factor-binding analysis
Language:R 17
WPZgithub / CEFCON
Deciphering driver regulators of cell fate decisions from single-cell RNA-seq data
attention-mechanism cell-fate deep-learning differentiation driver-regulators gene-regulatory-networks graph-neural-networks network-control single-cell-analysis
Language:Jupyter Notebook 15
AntoinePassemiers / PORTIA-Manuscript
Source code for the paper "Fast and Accurate Inference of Gene Regulatory Networks through Robust Precision Matrix Estimation", by Passemiers et al.
direct-coupling-analysis gaussian-graphical-models gene-regulatory-networks
Language:Python 7
calebclayreagor / DELAY
Depicting pseudotime-lagged causality for accurate gene-regulatory inference
gene-regulation deep-learning single-cell multi-omics gene-regulatory-network-inference gene-regulatory-networks
Language:Python 5
lab319 / GRNs_nonlinear_ODEs
gene-regulatory-networks
Language:Python 4
yukuntan92 / PALLAS
A tool for gene regulatory inference
inference gene-regulatory-networks
Language:Python 4
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
Neelhpatel2011 / GRN-reconstruction-RFR
Gene regulatory network reconstruction using random forest regression from only gene expression data from Single Cell RNA Seq Data. This project consisted of feature importance extraction and exploring different methods to investigate different and unique ways to extract feature importance to construct a gene regulatory network.
data-science gene-regulatory-networks healthcare machine-learning
Language:Jupyter Notebook 2
niaid / Gene_Regulatory_Networks
bcbb-training ace-uganda2020 gene-regulatory-networks webinar single-cell-rna-seq
Language:Jupyter Notebook 2
harissa-framework / harissa
Simulation and inference of gene regulatory networks based on transcriptional bursting
mechanistic-modeling gene-regulatory-networks single-cell-rna-seq
Language:Python 1
NYXFLOWER / DrugDiscovery
An explainable inductive learning model on gene regulatory and toxicogenomic knowledge graph (under development...)
gnn drug-discovery drug-design drug-repurposing molecular-mechanics explainable-ml predictive-models inductive-learning knowledge-graph heterogeneous-graph systems-biology gene-regulatory-networks new-dataset
Language:Jupyter Notebook 1
brismonis / PDF-to-Rules
Python Code to extract gene regulatory Information and create Boolean functions from PDFs using OCR and NLP, realized as a Django Website.
natural-language-processing optical-character-recognition django python3 gene-regulatory-networks boolean-function
Language:CSS 0
uds-helms / MutaNET
Automated analysis tool for mutations in promoters, transcription factor binding sites, coding regions and protein domains in the context of gene regulatory networks.
ngs mutations automated-analysis gene-regulatory-networks pipeline mutation-analysis converters protein-domains ngs-pipeline coding-regions transcription-factor-binding-site gui
Language:Python 0
amlalejini / ALife-2020--SignalGP-Genetic-Regulation
Supplemental material associated with ALife 2020 conference submission.
artificial-life genetic-programming artificial-gene-regulatory-networks gene-regulatory-networks signalgp evolutionary-computation
Language:HTML
javiegal / neurogenpy
Python package for estimating GRNs with Bayesian networks.
bayesian-networks gene-regulatory-networks humanbrainproject probabilistic-graphical-models python
Language:Python