Repositories list

• ontograph

  Public
  A lightweight Python package for loading, representing, and efficiently querying biological ontologies as graph structures.

  graphsontologiesbiological-networks

  Python

  •

  MIT License

  •0•0•1•0•Updated Jul 13, 2025Jul 13, 2025

• ParTIpy

  Public
  Pareto Task Inference in Python

  Python

  •

  GNU General Public License v3.0

  •0•0•0•1•Updated Jul 13, 2025Jul 13, 2025

• ParTIpy_paper

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jul 13, 2025Jul 13, 2025

• OmnipathR

  Public
  R client for the OmniPath web service

  proteinsnetworkspathways+ 4complexesnetworks-biologyomnipathenzyme-ptm

  R

  •

  Other

  •19•137•14•0•Updated Jul 12, 2025Jul 12, 2025

• MetaProViz

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

  R

  •

  GNU General Public License v3.0

  •3•15•13•1•Updated Jul 12, 2025Jul 12, 2025

• FUNKI

  Public
  FUNctional analysis worKflows Interface

  pythonworkflowanalysis+ 1omics

  Python

  •

  GNU General Public License v3.0

  •1•4•0•0•Updated Jul 11, 2025Jul 11, 2025

• incura_app

  Public
  Code for Streamlit application of incur

  Python

  •

  Creative Commons Zero v1.0 Universal

  •1•0•0•0•Updated Jul 11, 2025Jul 11, 2025

• saezlab.org

  Public
  TypeScript

  •0•0•1•0•Updated Jul 10, 2025Jul 10, 2025

• 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

  •48•145•10•0•Updated Jul 10, 2025Jul 10, 2025

• liana-py

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

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

  Python

  •

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

  •27•220•33•0•Updated Jul 9, 2025Jul 9, 2025

• GNNClinicalOutcomePrediction

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jul 7, 2025Jul 7, 2025

• QC_MALDIMSI

  Public
  Quality Control for MALDI-MSI

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 6, 2025Jul 6, 2025

• COSMOS_basic

  Public
  tutorial to use cosmosR in the context of basic downstream analysis of differential analysis or single sample.

  R

  •

  GNU General Public License v3.0

  •0•1•1•0•Updated Jul 6, 2025Jul 6, 2025

• cosmosR

  Public
  COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

  data-integrationproteomicsphosphoproteomics+ 3network-modellingtranscriptomicsmetabolomic-data

  R

  •

  GNU General Public License v3.0

  •16•61•7•0•Updated Jul 6, 2025Jul 6, 2025

• corneto

  Public
  Unified knowledge-driven network inference from omics data

  Python

  •

  GNU General Public License v3.0

  •7•44•4•0•Updated Jul 3, 2025Jul 3, 2025

• incura

  Public
  Python

  •1•0•0•0•Updated Jun 27, 2025Jun 27, 2025

• MultispectralHCC

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 27, 2025Jun 27, 2025

• omnipath

  Public
  Python client for the OmniPath web service

  Python

  •

  MIT License

  •8•45•7•0•Updated Jun 26, 2025Jun 26, 2025

• onionnet

  Public
  OnionNet

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

• lipinet

  Public
  LipiNet: A comprehensive tool for integrating and analyzing multilayer lipidomic networks. Leverage lipid interactions, pathways, and hierarchies to unlock insights into lipid metabolism and molecular functions.

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jun 17, 2025Jun 17, 2025

• reheat2_pub

  Public
  Multicellular Transcriptional Landscape of Heart Failure

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•1•0•Updated Jun 13, 2025Jun 13, 2025

• reheat2_shiny

  Public
  shiny app to access results from ReHeaT2

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 12, 2025Jun 12, 2025

• saezlab-resources-hub

  Public
  Kickstart your Software Engineering journey with this comprehensive resource hub, curated by the Saez-Rodriguez Group to support learning, best practices, and hands-on development.

  bioinformaticsbest-practicessoftware-engineering

  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 11, 2025Jun 11, 2025

• python-project

  Public
  Python project template

  Python

  •

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

  •1•0•0•1•Updated Jun 11, 2025Jun 11, 2025

• omnipath-server

  Public
  The OmniPath web API

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jun 6, 2025Jun 6, 2025

• F1000_Slack

  Public
  F the Bot

  slackbotsciwheel

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 6, 2025Jun 6, 2025

• mistyR

  Public
  Multiview Intercellular SpaTial modeling framework

  machine-learningmodularr+ 7biologyspatialbioconductormolecular-biologymultiviewspatial-transcriptomicsintercellular

  R

  •

  GNU General Public License v3.0

  •11•61•3•0•Updated Jun 6, 2025Jun 6, 2025

• CollecTRI

  Public
  Gene regulatory network containing signed transcription factor-target gene interactions

  R

  •

  GNU General Public License v3.0

  •8•84•0•0•Updated May 27, 2025May 27, 2025

• cheerio

  Public
  Shiny app to access cardiac hypertrophy data

  R

  •0•0•0•0•Updated May 22, 2025May 22, 2025

• omnipath-next

  Public
  A WebApp for the Omnipath database, allowing users to browse, filter and download data.

  TypeScript

  •0•0•0•0•Updated May 20, 2025May 20, 2025