Repositories list

• lab_website

  Public
  Our lab website

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •11 fork•11 star•00 issues•11 pull request•Updated May 25, 2026May 25, 2026

• MiRA

  Public
  This repository contains the code for MiRA: An app designed to visualize multilayer networks

  ecologyvisualizationsbiological-networks+ 1

  ecologyvisualizationsbiological-networksmultilayer-networks

  JavaScript

  •

  Other

  •00 forks•00 stars•99 issues•11 pull request•Updated May 21, 2026May 21, 2026

• figaro-

  Public
  HTML

  •00 forks•00 stars•1010 issues•00 pull requests•Updated May 20, 2026May 20, 2026

• spatial_prediction

  Public
  predicting links using softImpute

  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 19, 2026May 19, 2026

• emln

  Public
  An R package for handling and manipulating multilayer network data, mainly for ecological networks

  modelingdata-structuresecology+ 3

  modelingdata-structuresecologynetwork-analysisnetworksciencemultilayer-networks

  JavaScript

  •

  Creative Commons Attribution 4.0 International

  •22 forks•77 stars•00 issues•00 pull requests•Updated May 17, 2026May 17, 2026

• emln_package

  Public
  About emln: An R package that contains 78 ecological multilayer networks for analysis

  R

  •00 forks•00 stars•66 issues•00 pull requests•Updated May 10, 2026May 10, 2026

• infomap_ecology_package

  Public
  Package with functions to handle network data and run Infomap, inspired by ecological networks

  flowrr-package+ 5

  flowrr-packageecologynetwork-analysismultilayer-networkinfomapecological-networks

  R

  •22 forks•2828 stars•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• Norwood_farm

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 24, 2025Oct 24, 2025

• metabolic_corrs_networks_analysis

  Public
  This repository contains all the data and source code used to produce the results presented in the paper "Metabolite correlation networks reveal complex phenoty…

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 4, 2025Oct 4, 2025

• Microbiome_Structure_Madagascar

  Public
  Host-microbiome structure across land use change in Madagascar

  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 20, 2025Jul 20, 2025

• phylogenetic_rumen_prediction

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 14, 2025Jul 14, 2025

• eco_ILP

  Public
  Code and data for the paper "Inductive link prediction boosts data availability and enables cross-community link prediction in ecological networks"

  machine-learningpaperecology+ 2

  machine-learningpaperecologylink-predictionecological-networks

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 15, 2025Jun 15, 2025

• Sequential_LP

  Public
  We present a temporal optimal link prediction method that is based on the stacking link prediction method.

  Python

  •

  MIT License

  •33 forks•00 stars•00 issues•00 pull requests•Updated Jun 3, 2025Jun 3, 2025

• rumen_microbiome_structure

  Public
  this is a reiteration of microbiome_structure_v2 with cleaner folder tree and fixed intralayer edge weights.

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 26, 2024Aug 26, 2024

• spatial_modularity_in_the_canary_islands

  Public
  Code and data accompanying the paper "Local and regional processes drive distance decay in structure in a spatial multilayer plant-pollinator network"

  ecologymultilayer-networksecological-networks

  ecologymultilayer-networksecological-networks

  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 8, 2024Aug 8, 2024

• link_prediction_project

  Public
  Ofir and Eden Project of link prediction

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 18, 2024Jul 18, 2024

• cancer-networks

  Public
  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 28, 2024Mar 28, 2024

• Plasmid_multilayer_networks

  Public
  Data and scripts for analysis in Shapiro et al., "Multilayer Networks of Plasmid Genetic Similarity Reveal Potential Pathways of Gene Transmission"

  R

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 28, 2023Mar 28, 2023

• Poll_Seed-disp_Multilayer_Patagonia

  Public
  Codes and data to

  R

  •11 fork•11 star•00 issues•00 pull requests•Updated Jan 16, 2023Jan 16, 2023

• COVID19_vaccine_model

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 20, 2021Aug 20, 2021

• network-navigator

  Public
  Interactive hierarchical network navigator

  Python

  •

  MIT License

  •11 fork•00 stars•1111 issues•00 pull requests•Updated Jun 20, 2021Jun 20, 2021

• CRISPR_networks

  Public
  crisprbacteriaecology+ 5

  crisprbacteriaecologycrispr-cas9immunityspacervirus-strainsprotospacer

  R

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 5, 2020Aug 5, 2020