Discover saezlab/CellNOptR-MaBoSS Open Source project

Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.

139

pypath

R package to access DoRothEA's regulons

128

dorothea

120

liana-py

LIANA+: an all-in-one framework for cell-cell communication

R package for Pathway RespOnsive GENe activity inference

118

progeny

OmnipathR

R client for the OmniPath web service

visium_heart

Spatial transcriptomics of heart tissue

This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL

transcriptutorial

CARNIVAL

CAusal Reasoning for Network Identification with integer VALue programming in R

cosmosR

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 interactions

mistyR

Multiview Intercellular SpaTial modeling framework

omnipath

Python client for the OmniPath web service

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

FootprintMethods_on_scRNAseq

footprints

Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"

lipyd

Python module for lipidomics LC MS/MS data analysis

CORNETO: A Unified Omics-Driven Framework for Network Inference

corneto

FUNctional toolKIt platform for multi-omic functional analysis. An standardised pipeline to analysis transcriptomic, proteomic, phosphoproteomic and metabolomic datasets.

ShinyFUNKI

progeny-py

PROGENY Python implementation

Dorothea package in Python

dorothea-py

Code used for muti cellular factor analysis

MOFAcell

Toolbox for Kinase Activity Scoring based on phosphoproteomic data

kinact

R package for metabolic enzyme enrichment anaylsis

ocean

BioCypher

A unified language for biomedical research knowledge graphs

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.

CellNOptR

decoupleRBench

Package to benchmark methods from decoupleR

MOFAcellulaR

R package to infer multicellular programs from single-cell data using multi-omics factor analysis (MOFA)

SLAPenrich

Sample Level Analysis of Pathway Alteration Enrichments

PHONEMeS

PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is an R package to model signalling networks based on untargeted phosphoproteomics

decoupleR_manuscript

Code to reproduce the results from decoupleR's manuscript

eccb2022_sc_funcomics

Functional analysis of single-cell transcriptomics

a plug-in to access Omnipath from Cytoscape

Omnipath_Cytoscape

Java

scell_hfpef

single cell RNAseq analysis of HFpEF mice model

MetaProViz

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 platform

CKG-BioCypher

We use our tools to analysis Covid19 RNAseq datasets

DOT

Covid19

ligrec_decouple

Systematic Comparison of Cell-Cell Communication Tools and Resources

PerMedCoE_summer_school_2023

PerMedCoE summer school 2023

Tool for training of logic models of signalling networks using prior knowledge networks and perturbation data.

cellnopt

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 pharmacology

Bridging Cytoscape with R

cyrface

Java

FUNKI

FUNctional analysis worKflows Interface

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

VisiumMS

add-on for CellNOptR using logic based differential equations

kasumi_bench

CNORode

scheduling

Repository to collect issues for events to be scheduled

ST pipelines on mouse colon and small intestine

visium_colon_si

CNORode2017

modified version of CNORode including: steady state penalty, L1 regularisation, bootstrap, new transfer function

liverx

Analysis of liver proteomics data from Aebersold lab

Rich interface on top of the official Neo4j driver

neo4j-utils

cytocopter

CellNOptR in Cytoscape

Java

2023-SysBioCourse-ACSB

Teaching material for the single-cell course 2022

Singlecell_course_2022

ShinyCNOR

Shiny application for the CellNOptR packages

TumorDeconvolution

Estimate tumor purities from gene expression data

Mobi microbiome course materials

Microbiome_analysis_course_2022

Building and Training of the NicheNet Method exclusively using OmniPath resources. SARS-CoV-2 case study

NicheNet_Omnipath

PerMedCoE_tools_virtual_course_2023

Material for the PerMedCoE virtual course: transcriptomics to mechanistic models of signalling.

OTAR-BioCypher

snk-tutorial

Proteogenomics analsysis of protein attenuation in tumours

protein_attenuation

teaching material for various courses

teaching_material

Processing RNAseq data from Cell Lines. From raw data to normalised, voom and ComBat batch-correction

process_rnaseq_cellines

2024_EBI_GRN

Materials for the 2024 course at EMBL-EBI: "Modelling gene regulation from transcriptomics and chromatin accessibility single-cell data".

This is a short tutorial to show in parallel how to estimate TF and kinase activities from transcriptomic and phosphoproteomic data

kinase_tf_mini_tuto

Xu_tubuloid

Teaching material for 2022 SysBio Course

kinase_tf_mini_tuto_simple

2022-SysBioCourse-ACSB

teaching materials for the network modeling course

NetworkModeling_course_2020

Mutual information-based and bicor-based methods for genome-wide reverse engineering of gene regulatory networks in R.

gene-network-inference-in-R

liver-disease-atlas-app

ccc_protocols

LIANA x Tensor-cell2cell Protocols

MOON_example

analysis and visualization workflows for the OmniPath 2 paper

omnipath_analysis

Transcriptomic cross-species analysis of chronic liver disease reveals consistent regulation between humans and mice

meta_PKN_BIGG

liver-disease-atlas

Macau_Synergy_Prediction

Target functional similarity based workflows for drug synergy prediction and stratification

MedInfNetworks2022

modelling breast cancer cytof data with logic ODEs

breastCancerCytof

An R package implementing high-performing routines for the randomisation of bipartite graphs preserving their node degrees.

BiRewire

hepatic-microenviroment

Gut microbiota fuels HCC development by shaping the hepatic inflammatory microenvironment

network_tools

Collection of Python functions to run network-based analysis in signed and directed networks.

integration of omnipath causal network with STITCH and Recon3D

Meta_PKN

biocypher-project-template

Template for creating a BioCypher-driven knowledge graph

ILP implementation of PHONEMeS

PHONEMeS-ILP

CARNIVAL-Bioconductor-Dev

Provisional repository for the development of CARNIVAL package for Bioconductor

MedInfNetworks2021

simulator used for the Misty paper

CKD_Landscape

insilico_tissue_simulator

CNORprob

Probabilistic logic version of CellNOpt (derived from FALCON)

DrugVsDisease

DvD: An R and Cytoscape plug-in for comparing Drug and Disease profiles

recon3D_BIGG

Spatial space data from mouse

astromouse