Repositories list

• 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•134•14•0•Updated Nov 22, 2024Nov 22, 2024

• 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

  •2•2•14•0•Updated Nov 21, 2024Nov 21, 2024

• MetaProViz

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

  HTML

  •

  GNU General Public License v3.0

  •0•10•13•0•Updated Nov 21, 2024Nov 21, 2024

• omnipath-server

  Public
  The OmniPath web API

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• benchmarKIN

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• OmnipathR

  Public
  R client for the OmniPath web service

  proteinsnetworkspathways+ 4complexesnetworks-biologyomnipathenzyme-ptm

  R

  •

  Other

  •20•112•15•0•Updated Nov 20, 2024Nov 20, 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•3•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

• corneto

  Public
  Unified knowledge-driven network inference from omics data

  Python

  •

  GNU General Public License v3.0

  •3•26•4•1•Updated Nov 8, 2024Nov 8, 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•195•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

• cyrface

  Public
  Bridging Cytoscape with R

  Java

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

• kasumi_bench

  Public
  R

  •

  GNU General Public License v3.0

  •0•5•0•0•Updated Sep 25, 2024Sep 25, 2024

• CRCDiet

  Public
  CRCDiet

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

• 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

  •21•168•27•1•Updated Sep 21, 2024Sep 21, 2024

• GNNClinicalOutcomePrediction

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Sep 17, 2024Sep 17, 2024

• pypath-common

  Public
  Code shared across pypath modules

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Sep 10, 2024Sep 10, 2024

• 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

  •25•167•0•0•Updated Sep 10, 2024Sep 10, 2024

• liana

  Public
  LIANA: a LIgand-receptor ANalysis frAmework

  ligand-receptorcell-cell-communicationomnipath+ 3cellphonedbcellchatliana

  R

  •

  GNU General Public License v3.0

  •31•182•28•4•Updated Aug 7, 2024Aug 7, 2024

• flop

  Public
  FunctionaL Omics Processing platform

  R

  •

  GNU General Public License v3.0

  •1•13•1•0•Updated Jul 25, 2024Jul 25, 2024

• 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

  •15•58•5•0•Updated Jul 23, 2024Jul 23, 2024

• Factor_COSMOS

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

  HTML

  •0•7•0•0•Updated Jul 10, 2024Jul 10, 2024