Repositories list

• corneto

  Public
  Unified knowledge-driven network inference from omics data

  Python

  •

  GNU General Public License v3.0

  •11•93•3•0•Updated Feb 16, 2026Feb 16, 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…

  Jupyter Notebook

  •

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

  •0•5•0•0•Updated Feb 15, 2026Feb 15, 2026

• omnipath-metabo

  Public
  Compound database and metabolomics feature processing web service

  Python

  •

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

  •0•0•0•0•Updated Feb 15, 2026Feb 15, 2026

• ParTIpy_paper

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 13, 2026Feb 13, 2026

• ParTIpy

  Public
  Pareto Task Inference in Python

  Python

  •

  GNU General Public License v3.0

  •0•11•0•0•Updated Feb 13, 2026Feb 13, 2026

• download-manager

  Public
  Download manager for Python

  Python

  •

  GNU General Public License v3.0

  •0•0•2•0•Updated Feb 13, 2026Feb 13, 2026

• omnipath-server

  Public
  The OmniPath web API

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Feb 13, 2026Feb 13, 2026

• OmnipathR

  Public
  R client for the OmniPath web service

  proteinsnetworkspathways+ 4complexesnetworks-biologyomnipathenzyme-ptm

  R

  •

  Other

  •21•154•19•0•Updated Feb 12, 2026Feb 12, 2026

• greta

  Public
  Benchmark of GRNs using the GRETA pipeline

  Python

  •

  GNU General Public License v3.0

  •3•31•5•0•Updated Feb 11, 2026Feb 11, 2026

• MetaProViz

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

  R

  •

  Other

  •3•17•14•1•Updated Feb 10, 2026Feb 10, 2026

• cosmosR

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

  data-integrationproteomicsphosphoproteomics+ 3transcriptomicsnetwork-modellingmetabolomic-data

  R

  •

  GNU General Public License v3.0

  •16•65•7•0•Updated Feb 10, 2026Feb 10, 2026

• DOT

  Public
  DOT

  biologyoptimizationspatial+ 5multi-objective-optimizationfrank-wolfespatial-transcriptomicsgene-enrichmentcell-type-deconvolution

  R

  •

  GNU General Public License v3.0

  •0•9•1•0•Updated Feb 10, 2026Feb 10, 2026

• saezlab_core

  Public
  This is session handler, configuration and logging handler for Saezlab packages and applications.

  best-practicessoftware-engineering

  Python

  •

  MIT License

  •0•0•12•0•Updated Feb 9, 2026Feb 9, 2026

• 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 Feb 6, 2026Feb 6, 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

  •0•0•0•0•Updated Feb 5, 2026Feb 5, 2026

• MINA

  Public
  Multicellular INtegration Analysis

  Jupyter Notebook

  •

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

  •0•0•0•0•Updated Feb 5, 2026Feb 5, 2026

• reactors

  Public
  A blazing-fast parallel Python engine to simulate stochastic reaction networks, written in Rust

  Rust

  •

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

  •0•1•0•0•Updated Feb 5, 2026Feb 5, 2026

• saezlab.org

  Public
  TypeScript

  •0•0•1•0•Updated Feb 4, 2026Feb 4, 2026

• pypath

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

  pythondatabaseresource+ 4networkmolecular-biologypathwaygenetic-regulatory-network

  Python

  •

  GNU General Public License v3.0

  •49•157•12•1•Updated Jan 28, 2026Jan 28, 2026

• OCEAN_MCFA

  Public
  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 28, 2026Jan 28, 2026

• kidney_biopsies_ArchR

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 28, 2026Jan 28, 2026

• kidney_biopsies_MCFA

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 28, 2026Jan 28, 2026

• SpaCEy

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•5•0•0•Updated Jan 27, 2026Jan 27, 2026

• phosphonetworks

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 27, 2026Jan 27, 2026

• gretapy

  Public
  Package to evaluate gene regulatory networks (GRNs).

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 27, 2026Jan 27, 2026

• 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

  •29•269•27•1•Updated Jan 24, 2026Jan 24, 2026

• iupred

  Public
  Packaged version of the IUPRED2A and AIUPRED intrinsically disordered region prediction methods

  Python

  •

  Other

  •0•0•0•0•Updated Jan 22, 2026Jan 22, 2026

• python-project

  Public
  Python project template

  Python

  •

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

  •2•0•0•0•Updated Jan 22, 2026Jan 22, 2026

• tiedie

  Public
  Packaged Python 3 version of the old TieDIE

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jan 22, 2026Jan 22, 2026

• mistyR

  Public
  Multiview Intercellular SpaTial modeling framework

  machine-learningmodularr+ 7biologyspatialbioconductormolecular-biologymultiviewspatial-transcriptomicsintercellular

  R

  •

  GNU General Public License v3.0

  •13•71•2•0•Updated Jan 15, 2026Jan 15, 2026