Saez Lab

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253 repositories

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.
database resource network molecular-biology pathway genetic-regulatory-network python
Python
•
GNU General Public License v3.0
•47•134•14•0•Updated Nov 22, 2024Nov 22, 2024
kinase_benchmark
Public
Comparison of different methods for kinase activity estimation
R
•0•0•0•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
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GNU General Public License v3.0
•0•10•13•0•Updated Nov 21, 2024Nov 21, 2024
omnipath-server
Public
The OmniPath web API
Python
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GNU General Public License v3.0
•0•0•0•0•Updated Nov 21, 2024Nov 21, 2024
benchmarKIN
Public
R
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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
proteins networks pathways complexes networks-biology omnipath enzyme-ptm
R
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Other
•20•112•15•0•Updated Nov 20, 2024Nov 20, 2024
download-manager
Public
Download manager for Python
Python
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GNU General Public License v3.0
•0•0•0•0•Updated Nov 19, 2024Nov 19, 2024
FUNKI
Public
FUNctional analysis worKflows Interface
python workflow analysis omics
Python
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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
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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.
python set data-science database model plot
Python
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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.
r rstats r-package
R
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GNU General Public License v3.0
•24•194•6•0•Updated Oct 19, 2024Oct 19, 2024
metalinks_web
Public
Web interface to allow contextualization of metalinksKG
Python
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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
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GNU General Public License v3.0
•0•5•0•0•Updated Sep 25, 2024Sep 25, 2024
CRCDiet
Public
CRCDiet
Python
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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
python spatial single-cell single-cell-rna-seq ligand-receptor cell-cell-communication spatialomics
Python
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GNU General Public License v3.0
•21•167•27•1•Updated Sep 21, 2024Sep 21, 2024
GNNClinicalOutcomePrediction
Public
Jupyter Notebook
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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
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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.
python data-science bioinformatics enrichment numba transcriptomics single-cell enrichment-analysis spatial-transcriptomics
Python
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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-receptor cell-cell-communication omnipath cellphonedb cellchat liana
R
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GNU General Public License v3.0
•31•182•28•4•Updated Aug 7, 2024Aug 7, 2024
flop
Public
FunctionaL Omics Processing platform
R
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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-integration proteomics phosphoproteomics network-modelling transcriptomics metabolomic-data
R
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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