network-inference

There are 1 repository under network-inference topic.

saeyslab / nichenetr
NicheNet: predict active ligand-target links between interacting cells
cell-cell-communication data-integration gene-expression intercellular-communication ligand-receptor ligand-target network-inference rna-seq single-cell-omics single-cell-rna-seq
Language:R 585
JuliaDynamics / Associations.jl
Algorithms for quantifying associations, independence testing and causal inference from data.
causal-inference transfer-entropy cross-mapping predictive-asymmetry entropy mutual-information surrogate-data time-series julia julia-language distance-correlation hacktoberfest associations causal-graphs conditional-mutual-information independence-testing network-inference partial-mutual-information
Language:Julia 168
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 122
shellrow / netdev
Cross-platform library for network interface and gateway. Written in Rust.
rust rust-library rust-crate network network-inference gateway
Language:Rust 82
PLN-team / PLNmodels
A collection of Poisson lognormal models for multivariate count data analysis
poisson-lognormal-model count-data network-inference pca multivariate-analysis r-package
Language:R 57
fabian-sp / GGLasso
A Python package for General Graphical Lasso computation
graphical-lasso graphical-models latent-variable-models network-inference optimization
Language:Python 39
ryanjgallagher / core_periphery_sbm
Bayesian network models for inferring core-periphery structure
network-science stochastic-block-model network-inference community-detection core-periphery
Language:Python 37
fdtomasi / regain
REGAIN (Regularised Graphical Inference)
scikit-learn graphical-models network-inference machine-learning latent-variables time-series
Language:Jupyter Notebook 29
networkinference / ARNI
Algorithm for Revealing Network Interactions (ARNI) from nonlinear collective dynamics
network inferred-interactions dynamical-systems reconstruction oscillator reconstructing-networks inference network-inference network-reconstruction time-series
Language:HTML 29
lingfeiwang / findr
Fast Inference of Networks from Directed Regulations
bayesian-network dag directed-graph gene-regulation network-inference systems-biology
Language:C 22
hyu-ub / BayesNetBP
R package for inference in Bayesian networks.
bayesian-networks network-inference probabilistic-graphical-models conditional-gaussian
Language:R 20
paulveillard / cybersecurity-networking
An ongoing curated collection of awesome software, libraries, frameworks, talks & videos, best practices, learning tutorials and important practical resources about networking in cybersecurity
network networking network-analysis networks network-inference network-security network-server network-security-books network-automation network-tools network-service networking-application networking-concepts network-programming networking-labs network-scripting
Language:Python 20
praveenLT / java-selenium-intercept-network
A sample repo to help you intercept network with Selenium Java on LambdaTest cloud. Run your Java Selenium tests on LambdaTest platform.
chrome-devtools-protocol intercept-requests java lambdatest selenium selenium-java selenium-webdriver testing automation automation-testing example examples java-testing network-inference selenium-testing intercept-network
Language:Java 18
DIANE
OceaneCsn / DIANE
Dashboard for the Inference and Analysis of Networks from Expression data
r network-inference gene-expression analysis-workflows
Language:R 16
laser-institute / network-analysis
Social Network Analysis and STEM Education is designed to prepare researchers to apply network analysis in order to better understand and improve teaching and learning.
network-analysis data-visualization community-detection network-inference
Language:HTML 14
mims-harvard / fusenet
Network inference by fusing data from diverse distributions
graphical-models exponential-family heterogeneous-network network-inference diverse-distributions fusing-data
Language:Python 14
CABSEL / SINCERITIES
SINCERITIES is a tool for inferring gene regulatory networks from time-stamped cross-sectional single cell transcriptional expression profiles.
single-cell-analysis network-inference
13
cellmapslab / kimono
KiMONo is a network inference tool for multi-omics datasets. The multi-omics network is calculated by sparse-group-LASSO regression and can incorporate prior biological information using protein-protein Interactions.
data-integration network-inference multi-omic
Language:R 9
GemsLab / hashing-based-network-discovery
Hashing-based network discovery from time series
correlation time-series scalability lsh network-inference locality-sensitive-hashing network-discovery
Language:Python 8
callahantiff / owl-nets
Transforming OWL for statistical learning
semantic-web web-ontology-language network-inference sparql-query ontologies knowledge-graph hacktoberfest
Language:Python 7
pdesrosiers / GrangerCausality
MATLAB module for assessing the causal links between time series
timeseries-analysis network-inference computational-neuroscience granger-causality causality-analysis
Language:MATLAB 7
Roy-lab / merlin-p
A prior-based integrative framework for functional transcriptional regulatory network inference (Fotuhi Siahpirani & Roy, Nucleic Acids Research 2017)
network-inference clustering
Language:C 5
dongeric / time-varying-graphical-lasso-impl
Implementation of time-varying graphical lasso from research paper (2019)
python matlab network-inference convex-optimization
Language:Jupyter Notebook 4
effrosyni-papanastasiou / constrained-em
A constrained expectation-maximization algorithm for feasible graph inference.
expectation-maximization network-inference feasibility expectation-maximisation-algorithm inference-optimization
Language:Jupyter Notebook 4
le-ander / MSc_Bioinfo-Network_Inference
Network inference for gene expression using gradient matching. Final research project as part of the MSc in Bioinformatics and Theorectical Systems Biology at Imperial College London 2016/2017.
bioinformatics gaussian-processes gene-expression gradient-matching julia network-inference systems-biology
Language:Julia 4
newTypeGeek / Network-Reconstruction
Effect of hidden nodes on the reconstruction of bidirectional networks
network bidirectional-networks network-reconstruction inference network-inference clustering hidden-nodes dynamical-systems stochastic-differential-equations covariance-matrix inverse-covariance time-series
Language:Python 4
biolab / red
Inference of Epistatic Gene Networks
network-inference epistasis genetic-interactions mutant-data
Language:Python 3
GrossTor / IdentiFlow
Identifiability and experimental design in perturbation studies
identifiability network-inference reverse-engineering maximum-flow matroid experimental-design systems-biology
Language:Python 3
paubellot / netbenchmark
This package implements a benchmarking of several gene network inference algorithms from gene expression data
network network-inference gene-expression graph-and-network grn benchmark
Language:R 3
tallulandrews / scTarNet
network-inference single-cell-rna-seq
Language:R 3
cgao-comp / PBI
The code of the paper "Pairwise-interactions-based Bayesian Inference of Network Structure from Cascades"
bayesian-inference information-diffusion network-inference survival-analysis
Language:Python 2
dimitra-maoutsa / Connectivity_from_event_timing_patterns
Model-free method for inferring synaptic interactions from spike train recordings.
network-inference network-reconstruction spiking-neural-networks spikes inferring-synaptic-interactions synaptic-connectivity synaptic-interactions
Language:Python 2
networkinference / ESL
Network inference via Event Space Linearization (ESL)
network inference network-inference spikes spiking-neural-networks spiking-networks network-reconstruction reconstruction model-free neural-networks
Language:Python 2
plliao / FASTEN
FASTEN: the software to influence multiple diffusion networks using the first-hand sharing pattern.
machine-learning network-inference social-network
Language:C++ 2
Roy-lab / merlin
Regulatory network inference with module prior
network-inference clustering
Language:C 2
Roy-lab / mrtle
Multi-species regulatory network learning (Koch et al, Cell Systems 2017)
multi-task-learning network-inference
Language:C 2