Repositories list

• liana-py

  Public
  LIANA+: an all-in-one framework for cell-cell communication

  pythonspatialsingle-cell+ 4single-cell-rna-seqligand-receptorcell-cell-communicationspatialomics

  Python

  •

  GNU General Public License v3.0

  •22•177•24•0•Updated Jan 17, 2025Jan 17, 2025

• decoupler-py

  Public
  Python package to perform enrichment analysis from omics data.

  pythondata-sciencebioinformatics+ 6enrichmentnumbatranscriptomicssingle-cellenrichment-analysisspatial-transcriptomics

  Python

  •

  GNU General Public License v3.0

  •26•176•2•0•Updated Jan 17, 2025Jan 17, 2025

• greta

  Public
  Benchmark of GRNs using the GRETA pipeline

  Python

  •

  GNU General Public License v3.0

  •0•10•0•0•Updated Jan 17, 2025Jan 17, 2025

• corneto

  Public
  Unified knowledge-driven network inference from omics data

  Python

  •

  GNU General Public License v3.0

  •3•29•5•0•Updated Jan 16, 2025Jan 16, 2025

• networkcommons

  Public
  NetworkCommons is a community-driven platform designed to simplify access to tools and resources for inferring context-specific protein interaction networks by integrating context-agnostic prior knowledge with omics data.

  Python

  •

  GNU General Public License v3.0

  •3•10•14•1•Updated Jan 15, 2025Jan 15, 2025

• MetaProViz

  Public
  R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.

  HTML

  •

  GNU General Public License v3.0

  •1•13•13•0•Updated Jan 15, 2025Jan 15, 2025

• omnipath-server

  Public
  The OmniPath web API

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

• corneto-manuscript-experiments

  Public
  Results using CORNETO, included in the manuscript

  Jupyter Notebook

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• CRCDiet

  Public
  CRCDiet

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 9, 2025Jan 9, 2025

• F1000_Slack

  Public
  F the Bot

  slackbotsciwheel

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 8, 2025Jan 8, 2025

• VisiumMS

  Public
  Study of Multiple Sclerosis(MS) using paried snRNA-seq and Visium transcriptmics datasets.

  Python

  •

  GNU General Public License v3.0

  •5•6•0•0•Updated Dec 11, 2024Dec 11, 2024

• kasumi_bench

  Public
  R

  •

  GNU General Public License v3.0

  •0•5•0•0•Updated Dec 11, 2024Dec 11, 2024

• GNNClinicalOutcomePrediction

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Dec 10, 2024Dec 10, 2024

• benchmarKIN

  Public
  R

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Dec 5, 2024Dec 5, 2024

• MedInfNetworks2024

  Public
  HTML

  •0•0•0•0•Updated Dec 5, 2024Dec 5, 2024

• saezverse

  Public
  Docker image with all tools from the lab

  Shell

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• OmnipathR

  Public
  R client for the OmniPath web service

  proteinsnetworkspathways+ 4complexesnetworks-biologyomnipathenzyme-ptm

  R

  •

  Other

  •20•124•19•0•Updated Dec 1, 2024Dec 1, 2024

• kinase_benchmark

  Public
  Comparison of different methods for kinase activity estimation

  R

  •0•0•0•0•Updated Nov 25, 2024Nov 25, 2024

• omnipath-metabo

  Public
  Utilities for metabolite processing

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 22, 2024Nov 22, 2024

• pypath

  Public
  Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.

  databaseresourcenetwork+ 4molecular-biologypathwaygenetic-regulatory-networkpython

  Python

  •

  GNU General Public License v3.0

  •47•137•14•0•Updated Nov 22, 2024Nov 22, 2024

• download-manager

  Public
  Download manager for Python

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• FUNKI

  Public
  FUNctional analysis worKflows Interface

  pythonworkflowanalysis+ 1omics

  Python

  •

  GNU General Public License v3.0

  •1•4•0•0•Updated Nov 17, 2024Nov 17, 2024

• cache-manager

  Public
  A Python cache manager

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• ocean

  Public
  R package for metabolic enzyme enrichment anaylsis

  R

  •

  GNU General Public License v3.0

  •4•11•0•0•Updated Nov 8, 2024Nov 8, 2024

• reheat2_pub

  Public
  Multicellular Transcriptional Landscape of Heart Failure

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

• data_tools

  Public
  Collection of Python functions and classes designed to make data scientists' life easier.

  pythonsetdata-science+ 3databasemodelplot

  Python

  •

  GNU General Public License v3.0

  •5•4•0•0•Updated Oct 22, 2024Oct 22, 2024

• decoupleR

  Public
  R package to infer biological activities from omics data using a collection of methods.

  rrstatsr-package

  R

  •

  GNU General Public License v3.0

  •24•218•6•0•Updated Oct 19, 2024Oct 19, 2024

• metalinks_web

  Public
  Web interface to allow contextualization of metalinksKG

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

• kidneyfibrosis_multiomicsmodel_paper

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024

• cytocopter

  Public
  CellNOptR in Cytoscape

  Java

  •2•2•3•1•Updated Oct 3, 2024Oct 3, 2024