Repositories list

• 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 Mar 9, 2025Mar 9, 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•59•6•0•Updated Mar 9, 2025Mar 9, 2025

• omnipath-server

  Public
  The OmniPath web API

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Mar 7, 2025Mar 7, 2025

• F1000_Slack

  Public
  F the Bot

  slackbotsciwheel

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 6, 2025Mar 6, 2025

• greta

  Public
  Benchmark of GRNs using the GRETA pipeline

  Python

  •

  GNU General Public License v3.0

  •0•17•0•0•Updated Mar 5, 2025Mar 5, 2025

• kidneyfibrosis_multiomicsmodel_paper

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Mar 5, 2025Mar 5, 2025

• omnipath

  Public
  Python client for the OmniPath web service

  Python

  •

  MIT License

  •7•43•6•0•Updated Mar 3, 2025Mar 3, 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

  •2•13•13•0•Updated Feb 28, 2025Feb 28, 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•138•14•0•Updated Feb 27, 2025Feb 27, 2025

• .github

  Public
  Python

  •6•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• kasumi_bench

  Public
  R

  •

  GNU General Public License v3.0

  •0•5•0•0•Updated Feb 20, 2025Feb 20, 2025

• 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•229•8•0•Updated Feb 14, 2025Feb 14, 2025

• GNNClinicalOutcomePrediction

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Feb 14, 2025Feb 14, 2025

• OmnipathR

  Public
  R client for the OmniPath web service

  proteinsnetworkspathways+ 4complexesnetworks-biologyomnipathenzyme-ptm

  R

  •

  Other

  •20•126•14•0•Updated Feb 25, 2025Feb 25, 2025

• 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

  •23•190•24•0•Updated Feb 13, 2025Feb 13, 2025

• benchmarKIN

  Public
  R

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Feb 11, 2025Feb 11, 2025

• corneto

  Public
  Unified knowledge-driven network inference from omics data

  Python

  •

  GNU General Public License v3.0

  •3•32•5•0•Updated Feb 8, 2025Feb 8, 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

  •27•181•1•0•Updated Feb 7, 2025Feb 7, 2025

• saezlab.org-next

  Public
  Playground for a new lab web site

  Astro

  •

  MIT License

  •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

• kinase_benchmark

  Public
  Comparison of different methods for kinase activity estimation

  R

  •0•0•0•0•Updated Feb 5, 2025Feb 5, 2025

• cheerio

  Public
  Shiny app to access cardiac hypertrophy data

  R

  •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

• MetalinksDB

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Jan 23, 2025Jan 23, 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

  •4•19•14•2•Updated Jan 22, 2025Jan 22, 2025

• FUNKI

  Public
  FUNctional analysis worKflows Interface

  pythonworkflowanalysis+ 1omics

  Python

  •

  GNU General Public License v3.0

  •1•4•0•0•Updated Jan 20, 2025Jan 20, 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

• VisiumMS

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

  Python

  •

  GNU General Public License v3.0

  •5•6•1•0•Updated Dec 11, 2024Dec 11, 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

• omnipath-metabo

  Public
  Utilities for metabolite processing

  Python

  •

  GNU General Public License v3.0

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