PLN-team/PLNmodels

A collection of Poisson lognormal models for multivariate count data analysis

Language: R - Size: 110 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 55 - Forks: 18

hyu-ub/BayesNetBP

R package for inference in Bayesian networks.

Language: R - Size: 5.57 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 20 - Forks: 3

shellrow/netdev

Cross-platform library for network interface and gateway. Written in Rust.

Language: Rust - Size: 289 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 73 - Forks: 19

saeyslab/nichenetr

NicheNet: predict active ligand-target links between interacting cells

Language: R - Size: 152 MB - Last synced at: 8 days ago - Pushed at: 11 days ago - Stars: 540 - Forks: 125

dimitra-maoutsa/inferring-synaptic-interactions-and-transmission-delays

Size: 6.52 MB - Last synced at: 11 days ago - Pushed at: 12 days ago - Stars: 1 - Forks: 0

simahashemi/Network-Inference-Random-Matrix-Models

Implements the Cavity Method on a 1D Ising model, derives the Wigner semicircle law via Random Matrix Theory, and explores electron conduction in disordered systems using the Anderson model.

Language: Python - Size: 1.13 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0

fullscreen-triangle/hegel

Evidence Rectification Framework for Biological Molecules

Language: JavaScript - Size: 2.11 MB - Last synced at: 20 days ago - Pushed at: 21 days ago - Stars: 1 - Forks: 0

pinellolab/dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

Language: Python - Size: 25 MB - Last synced at: about 8 hours ago - Pushed at: 9 months ago - Stars: 117 - Forks: 15

fabian-sp/GGLasso

A Python package for General Graphical Lasso computation

Language: Python - Size: 122 MB - Last synced at: 2 days ago - Pushed at: 3 months ago - Stars: 35 - Forks: 14

JuliaDynamics/Associations.jl

Algorithms for quantifying associations, independence testing and causal inference from data.

Language: Julia - Size: 54.7 MB - Last synced at: 14 days ago - Pushed at: about 2 months ago - Stars: 156 - Forks: 15

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

Language: Python - Size: 954 KB - Last synced at: about 2 months ago - Pushed at: almost 3 years ago - Stars: 14 - Forks: 4

callahantiff/owl-nets

Transforming OWL for statistical learning

Language: Python - Size: 54.1 MB - Last synced at: 2 months ago - Pushed at: over 4 years ago - Stars: 7 - Forks: 2

CABSEL/SINCERITIES

SINCERITIES is a tool for inferring gene regulatory networks from time-stamped cross-sectional single cell transcriptional expression profiles.

Size: 16.6 MB - Last synced at: about 2 months ago - Pushed at: over 7 years ago - Stars: 13 - Forks: 5

fdtomasi/regain-applications

Containers for notebooks and data where REGAIN has been used.

Language: Jupyter Notebook - Size: 8.66 MB - Last synced at: 9 days ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

fdtomasi/regain

REGAIN (Regularised Graphical Inference)

Language: Jupyter Notebook - Size: 52.6 MB - Last synced at: 2 days ago - Pushed at: almost 2 years ago - Stars: 29 - Forks: 13

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.

Language: HTML - Size: 294 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 12 - Forks: 41

OceaneCsn/DIANE

Dashboard for the Inference and Analysis of Networks from Expression data

Language: R - Size: 106 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 4

GrossTor/IdentiFlow

Identifiability and experimental design in perturbation studies

Language: Python - Size: 92.8 KB - Last synced at: 2 months ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 0

dongeric/time-varying-graphical-lasso-impl

Implementation of time-varying graphical lasso from research paper (2019)

Language: Jupyter Notebook - Size: 5.65 MB - Last synced at: 11 months ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 2

tallulandrews/scTarNet

Language: R - Size: 2.16 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 1

Davide95/msc_thesis

Learning relational models from networked data on the web

Language: Jupyter Notebook - Size: 11.1 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

ryanjgallagher/core_periphery_sbm

Bayesian network models for inferring core-periphery structure

Language: Python - Size: 31.3 KB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 34 - Forks: 2

lucamasera/pyPCalg

Python wrapper of the PC++ skeleton function

Language: C++ - Size: 286 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

CyberCommands/PyInterface

Language: Python - Size: 11.7 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

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.

Language: Julia - Size: 47.9 KB - Last synced at: 2 months ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 3

lingfeiwang/findr

Fast Inference of Networks from Directed Regulations

Language: C - Size: 1.77 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 21 - Forks: 4

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.

Language: R - Size: 4.88 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 10 - Forks: 3

cgao-comp/PBI

The code of the paper "Pairwise-interactions-based Bayesian Inference of Network Structure from Cascades"

Language: Python - Size: 209 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

Roy-lab/mrtle

Multi-species regulatory network learning (Koch et al, Cell Systems 2017)

Language: C - Size: 40.3 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 2

paubellot/netbenchmark

This package implements a benchmarking of several gene network inference algorithms from gene expression data

Language: R - Size: 91.8 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 2

networkinference/ESL

Network inference via Event Space Linearization (ESL)

Language: Python - Size: 570 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 2 - Forks: 0

networkinference/ARNI

Algorithm for Revealing Network Interactions (ARNI) from nonlinear collective dynamics

Language: HTML - Size: 162 KB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 21 - Forks: 6

CABSEL/TRaCE

Transitive Reduction and Closure Ensemble

Language: Matlab - Size: 97.5 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 0

CABSEL/REDUCE

REDUCE is an algorithm for optimal design of gene knock-out (KO) for the purpose of gene regulatory network (GRN) inference.

Size: 43.9 KB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

xiaohan2012/active-infection-source-finding

Language: Jupyter Notebook - Size: 19.9 MB - Last synced at: 2 months ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 1

GemsLab/hashing-based-network-discovery

Hashing-based network discovery from time series

Language: Python - Size: 137 KB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 8 - Forks: 3

mims-harvard/fusenet

Network inference by fusing data from diverse distributions

Language: Python - Size: 255 KB - Last synced at: about 1 year ago - Pushed at: over 8 years ago - Stars: 14 - Forks: 7

Roy-lab/MERLIN-VIZ

A visualization toolset for MERLIN Networks. Allows for direct user interaction.

Language: R - Size: 16.5 MB - Last synced at: 8 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

newTypeGeek/Network-Reconstruction 📦

Effect of hidden nodes on the reconstruction of bidirectional networks

Language: Python - Size: 450 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 1

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.

Language: Java - Size: 8.79 KB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 18 - Forks: 7

Fjeanneret/multiSight

:bar_chart: :clipboard: Bioconductor R package with Graphical Interface to handle multi-omic data by Classification, Enrichment and Network inference.

Language: R - Size: 3.64 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 1

Roy-lab/merlin

Regulatory network inference with module prior

Language: C - Size: 140 KB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0

effrosyni-papanastasiou/constrained-em

A constrained expectation-maximization algorithm for feasible graph inference.

Language: Jupyter Notebook - Size: 16.6 KB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

dimitra-maoutsa/Connectivity_from_event_timing_patterns

Model-free method for inferring synaptic interactions from spike train recordings.

Language: Python - Size: 4.22 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

pdesrosiers/GrangerCausality

MATLAB module for assessing the causal links between time series

Language: Matlab - Size: 9.77 KB - Last synced at: over 2 years ago - Pushed at: almost 7 years ago - Stars: 2 - Forks: 0

GrossTor/response-logic

A network inference method based on a simple response logic with minimal presumptions

Language: Python - Size: 110 KB - Last synced at: 2 months ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

plliao/FASTEN

FASTEN: the software to influence multiple diffusion networks using the first-hand sharing pattern.

Language: C++ - Size: 1.89 MB - Last synced at: 3 months ago - Pushed at: about 8 years ago - Stars: 2 - Forks: 1

cpauvert/PLNnetwork-workflow

Infer network from count data within Snakemake using a sparse Poisson lognormal model (PLNnetwork)

Language: R - Size: 24.4 KB - Last synced at: about 2 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

Roy-lab/MERLIN-P-TFA_old_code

Language: C - Size: 10.2 MB - Last synced at: over 2 years ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0

Roy-lab/merlin-p

A prior-based integrative framework for functional transcriptional regulatory network inference (Fotuhi Siahpirani & Roy, Nucleic Acids Research 2017)

Language: C - Size: 5.87 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 7

biomedical-cybernetics/PC-corr_net

Language: R - Size: 3 MB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 1

Roy-lab/integrative_networks

Code for Chasman et al, PLOS Comp Biol 2016.

Language: GAMS - Size: 9.88 MB - Last synced at: over 2 years ago - Pushed at: almost 8 years ago - Stars: 1 - Forks: 1

biolab/red

Inference of Epistatic Gene Networks

Language: Python - Size: 2.88 MB - Last synced at: about 1 year ago - Pushed at: almost 11 years ago - Stars: 3 - Forks: 2