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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 communicationOmnipathR
R client for the OmniPath web serviceprogeny
R package for Pathway RespOnsive GENe activity inferencevisium_heart
Spatial transcriptomics of heart tissueCARNIVAL
CAusal Reasoning for Network Identification with integer VALue programming in Rtranscriptutorial
This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVALcosmosR
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 EnrichmentsdecoupleR_manuscript
Code to reproduce the results from decoupleR's manuscripteccb2022_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 datasetskasumi_bench
ligrec_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.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-correction2024_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