Repositories list

• ParTIpy

  Public
  Pareto Task Inference in Python

  Python

  •

  GNU General Public License v3.0

  •11 fork•2323 stars•00 issues•11 pull request•Updated Aug 10, 2026Aug 10, 2026

• annnet

  Public
  AnnNet (Annotated Network) is a unified, high-expressivity graph platform designed to bring the convenience of AnnData-style annotated containers to networks, m…

  pythongraphsystems-biology+ 12

  pythongraphsystems-biologyannotationscomputational-biologyinteroperabilityscientific-computingnetwork-analysisgraph-datasparse-matrix+ 5

  Python

  •

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

  •00 forks•1919 stars•00 issues•00 pull requests•Updated Aug 10, 2026Aug 10, 2026

• corneto

  Public
  Unified knowledge-driven network inference from omics data

  optimizationgraphsconstrained-optimization+ 6

  optimizationgraphsconstrained-optimizationmilpomicsnetwork-analysiscvxpybiological-networksomics-data-integration

  Python

  •

  GNU General Public License v3.0

  •99 forks•105105 stars•11 issue•00 pull requests•Updated Aug 7, 2026Aug 7, 2026

• MetaProViz

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

  R

  •

  Other

  •33 forks•2222 stars•1515 issues•11 pull request•Updated Aug 7, 2026Aug 7, 2026

• omnipath-present

  Public
  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 7, 2026Aug 7, 2026

• omnipath-client

  Public
  Python client for the new OmniPath web APIs

  bioinformaticstaxonomygene-regulation+ 6

  bioinformaticstaxonomygene-regulationnetworksmetabolomicsphosphoproteomicssignalingtranscriptomicsprior-knowledge

  Python

  •

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

  •00 forks•00 stars•00 issues•11 pull request•Updated Aug 7, 2026Aug 7, 2026

• heart_revremod_paper

  Public
  Bulk and single-nucleus RNA-seq analysis of mouse models of adverse and reverse cardiac remodeling

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 6, 2026Aug 6, 2026

• pypath

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

  pythondatabaseresource+ 4

  pythondatabaseresourcenetworkmolecular-biologypathwaygenetic-regulatory-network

  Python

  •

  GNU General Public License v3.0

  •5656 forks•165165 stars•1212 issues•00 pull requests•Updated Aug 5, 2026Aug 5, 2026

• saezlab.org

  Public
  TypeScript

  •00 forks•00 stars•11 issue•00 pull requests•Updated Aug 4, 2026Aug 4, 2026

• OmnipathR

  Public
  R client for the OmniPath web service

  proteinsnetworkspathways+ 4

  proteinsnetworkspathwayscomplexesnetworks-biologyomnipathenzyme-ptm

  R

  •

  Other

  •2525 forks•171171 stars•2222 issues•11 pull request•Updated Aug 3, 2026Aug 3, 2026

• omnipath-utils

  Public
  Prior-knowledge processing utilities Python package, database and web API

  taxonomyproteinsgenes+ 4

  taxonomyproteinsgenesdrugsomicsorthologsmetabolites

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 2, 2026Aug 2, 2026

• omnipath-build

  Public
  A general database builder on top of pypath.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 2, 2026Aug 2, 2026

• MINA

  Public
  Multicellular INtegration Analysis

  Python

  •

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

  •22 forks•55 stars•00 issues•22 pull requests•Updated Jul 31, 2026Jul 31, 2026

• cosmosR

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

  data-integrationproteomicsphosphoproteomics+ 3

  data-integrationproteomicsphosphoproteomicstranscriptomicsnetwork-modellingmetabolomic-data

  R

  •

  GNU General Public License v3.0

  •1717 forks•7070 stars•77 issues•00 pull requests•Updated Jul 28, 2026Jul 28, 2026

• snRNASeq_Brain_Tumor_Data_Analysis

  Public
  Analysis of single nucleus-RNAseq Brain Dataset - Stefan Pfister

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• omnipath-server

  Public
  The OmniPath web API

  Python

  •

  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• MOON_benchmark

  Public
  HTML

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• Factor_COSMOS

  Public
  Formatting NCI60 data into cosmos ready inputs and generation of testable hypothesis connecting cell-line specific TF and metabolic deregulations.

  HTML

  •00 forks•1212 stars•11 issue•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• liana-py

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

  pythonspatialsingle-cell+ 4

  pythonspatialsingle-cellsingle-cell-rna-seqligand-receptorcell-cell-communicationspatialomics

  Python

  •

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

  •3636 forks•310310 stars•2727 issues•44 pull requests•Updated Jul 16, 2026Jul 16, 2026

• omnipath-metabo

  Public
  Compound database and metabolomics feature processing web service

  Python

  •

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

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 15, 2026Jul 15, 2026

• pkg-infra

  Public
  Session, config and log handler for Saezlab Python packages

  best-practicessoftware-engineering

  best-practicessoftware-engineering

  Python

  •

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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 10, 2026Jul 10, 2026

• dlmachine

  Public
  Download manager for Python

  Python

  •

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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 10, 2026Jul 10, 2026

• kidney_biopsies_MCFA

  Public
  R

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 9, 2026Jul 9, 2026

• networkcommons

  Public
  NetworkCommons is a community-driven platform designed to simplify access to tools and resources for inferring context-specific protein interaction networks by …

  Python

  •

  GNU General Public License v3.0

  •77 forks•3434 stars•1717 issues•33 pull requests•Updated Jun 27, 2026Jun 27, 2026

• pypath-common

  Public
  Code shared across pypath modules

  Python

  •

  GNU General Public License v3.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Jun 24, 2026Jun 24, 2026

• gretapy

  Public
  Package to analyse and evaluate gene regulatory networks (GRNs).

  Python

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Jun 22, 2026Jun 22, 2026

• ProClaim

  Public
  Official code "ProClaim: Sufficiency-Aware Evidence Programming for In-the-Wild Scientific Claim Verification"

  Python

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Jun 22, 2026Jun 22, 2026

• gonads_snRNAseq_and_lipidomics_analysis_refactored

  Public
  Multi-omic analysis of gonadal hormone coordination in liver physiology using FCG mouse model

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 19, 2026Jun 19, 2026

• metabo-usecases

  Public
  Case studies for OmniPath Metabo manuscript

  R

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 18, 2026Jun 18, 2026

• cachedir

  Public
  A Python cache manager

  Python

  •

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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 15, 2026Jun 15, 2026