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decoupleR
R package to infer biological activities from omics data using a collection of methods.liana
LIANA: a LIgand-receptor ANalysis frAmeworkdecoupler-py
Python package to perform enrichment analysis from omics data.pypath
Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.dorothea
R package to access DoRothEA's regulonsliana-py
LIANA+: an all-in-one framework for cell-cell communicationprogeny
R package for Pathway RespOnsive GENe activity inferenceOmnipathR
R client for the OmniPath web servicevisium_heart
Spatial transcriptomics of heart tissuetranscriptutorial
This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVALCARNIVAL
CAusal Reasoning for Network Identification with integer VALue programming in RcosmosR
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.CollecTRI
Gene regulatory network containing signed transcription factor-target gene interactionsmistyR
Multiview Intercellular SpaTial modeling frameworkomnipath
Python client for the OmniPath web serviceFootprintMethods_on_scRNAseq
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq datafootprints
Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"lipyd
Python module for lipidomics LC MS/MS data analysiscorneto
CORNETO: A Unified Omics-Driven Framework for Network InferenceShinyFUNKI
FUNctional toolKIt platform for multi-omic functional analysis. An standardised pipeline to analysis transcriptomic, proteomic, phosphoproteomic and metabolomic datasets.progeny-py
PROGENY Python implementationdorothea-py
Dorothea package in PythonMOFAcell
Code used for muti cellular factor analysiskinact
Toolbox for Kinase Activity Scoring based on phosphoproteomic dataocean
R package for metabolic enzyme enrichment anaylsisBioCypher
A unified language for biomedical research knowledge graphsCellNOptR
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.decoupleRBench
Package to benchmark methods from decoupleRMOFAcellulaR
R package to infer multicellular programs from single-cell data using multi-omics factor analysis (MOFA)SLAPenrich
Sample Level Analysis of Pathway Alteration Enrichmentseccb2022_sc_funcomics
Functional analysis of single-cell transcriptomicsPHONEMeS
PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is an R package to model signalling networks based on untargeted phosphoproteomicsOmnipath_Cytoscape
a plug-in to access Omnipath from Cytoscapescell_hfpef
single cell RNAseq analysis of HFpEF mice modelMetaProViz
R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.Factor_COSMOS
Formatting NCI60 data into cosmos ready inputs and generation of testable hypothesis connecting cell-line specific TF and metabolic deregulations.flop
FunctionaL Omics Processing platformCKG-BioCypher
DOT
DOTCovid19
We use our tools to analysis Covid19 RNAseq datasetsligrec_decouple
Systematic Comparison of Cell-Cell Communication Tools and ResourcesPerMedCoE_summer_school_2023
PerMedCoE summer school 2023cellnopt
Tool for training of logic models of signalling networks using prior knowledge networks and perturbation data.HF_meta-analysis
Code that generates results and figures from: "A Consensus Transcriptional Landscape of Human End-Stage Heart Failure"CPT_QSPtutorial
Supplementary material for CPT tutorial on logic modeling for quantitative systems pharmacologycyrface
Bridging Cytoscape with RFUNKI
FUNctional analysis worKflows InterfaceVisiumMS
Study of Multiple Sclerosis(MS) using paried snRNA-seq and Visium transcriptmics datasets.kasumi_bench
CNORode
add-on for CellNOptR using logic based differential equationsscheduling
Repository to collect issues for events to be scheduledvisium_colon_si
ST pipelines on mouse colon and small intestineCellNOptR-MaBoSS
CellNOptR with MaBoSS simulationCNORode2017
modified version of CNORode including: steady state penalty, L1 regularisation, bootstrap, new transfer functionliverx
Analysis of liver proteomics data from Aebersold labneo4j-utils
Rich interface on top of the official Neo4j drivercytocopter
CellNOptR in Cytoscape2023-SysBioCourse-ACSB
Singlecell_course_2022
Teaching material for the single-cell course 2022ShinyCNOR
Shiny application for the CellNOptR packagesTumorDeconvolution
Estimate tumor purities from gene expression dataMicrobiome_analysis_course_2022
Mobi microbiome course materialsNicheNet_Omnipath
Building and Training of the NicheNet Method exclusively using OmniPath resources. SARS-CoV-2 case studyPerMedCoE_tools_virtual_course_2023
Material for the PerMedCoE virtual course: transcriptomics to mechanistic models of signalling.OTAR-BioCypher
snk-tutorial
protein_attenuation
Proteogenomics analsysis of protein attenuation in tumoursteaching_material
teaching material for various coursesprocess_rnaseq_cellines
Processing RNAseq data from Cell Lines. From raw data to normalised, voom and ComBat batch-correctionTFbenchmark
This repository contains the code used to benchmark TF-target datasets via TF activities in 3 benchmark datasets2024_EBI_GRN
Materials for the 2024 course at EMBL-EBI: "Modelling gene regulation from transcriptomics and chromatin accessibility single-cell data".kinase_tf_mini_tuto
This is a short tutorial to show in parallel how to estimate TF and kinase activities from transcriptomic and phosphoproteomic dataXu_tubuloid
kinase_tf_mini_tuto_simple
2022-SysBioCourse-ACSB
Teaching material for 2022 SysBio CourseNetworkModeling_course_2020
teaching materials for the network modeling coursegene-network-inference-in-R
Mutual information-based and bicor-based methods for genome-wide reverse engineering of gene regulatory networks in R.liver-disease-atlas-app
ccc_protocols
LIANA x Tensor-cell2cell ProtocolsMOON_example
omnipath_analysis
analysis and visualization workflows for the OmniPath 2 papermeta_PKN_BIGG
liver-disease-atlas
Transcriptomic cross-species analysis of chronic liver disease reveals consistent regulation between humans and miceMacau_Synergy_Prediction
Target functional similarity based workflows for drug synergy prediction and stratificationMedInfNetworks2022
breastCancerCytof
modelling breast cancer cytof data with logic ODEsBiRewire
An R package implementing high-performing routines for the randomisation of bipartite graphs preserving their node degrees.hepatic-microenviroment
Gut microbiota fuels HCC development by shaping the hepatic inflammatory microenvironmentnetwork_tools
Collection of Python functions to run network-based analysis in signed and directed networks.Meta_PKN
integration of omnipath causal network with STITCH and Recon3Dbiocypher-project-template
Template for creating a BioCypher-driven knowledge graphPHONEMeS-ILP
ILP implementation of PHONEMeSCARNIVAL-Bioconductor-Dev
Provisional repository for the development of CARNIVAL package for BioconductorMedInfNetworks2021
CKD_Landscape
insilico_tissue_simulator
simulator used for the Misty paperCNORprob
Probabilistic logic version of CellNOpt (derived from FALCON)DrugVsDisease
DvD: An R and Cytoscape plug-in for comparing Drug and Disease profilesrecon3D_BIGG
astromouse
Spatial space data from mouseLove Open Source and this site? Check out how you can help us