Discover saezlab/CellNOptR Open Source project by Saez Lab (@saezlab)

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

158

liana-py

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

156

pypath

R package to access DoRothEA's regulons

134

dorothea

132

OmnipathR

R client for the OmniPath web service

101

progeny

R package for Pathway RespOnsive GENe activity inference

visium_heart

Spatial transcriptomics of heart tissue

CAusal Reasoning for Network Identification with integer VALue programming in R

CARNIVAL

cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

transcriptutorial

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

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"

corneto

Unified knowledge-driven network inference from omics data

Python module for lipidomics LC MS/MS data analysis

lipyd

FunctionaL Omics Processing platform

flop

ShinyFUNKI

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

progeny-py

PROGENY Python implementation

Dorothea package in Python

dorothea-py

Code used for muti cellular factor analysis

MOFAcell

R package for metabolic enzyme enrichment anaylsis

ocean

kinact

Toolbox for Kinase Activity Scoring based on phosphoproteomic data

A unified language for biomedical research knowledge graphs

BioCypher

Sample Level Analysis of Pathway Alteration Enrichments

SLAPenrich

DOT

decoupleRBench

Package to benchmark methods from decoupleR

MOFAcellulaR

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

MetaProViz

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

Code to reproduce the results from decoupleR's manuscript

decoupleR_manuscript

eccb2022_sc_funcomics

Functional analysis of single-cell transcriptomics

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

PHONEMeS

Omnipath_Cytoscape

a plug-in to access Omnipath from Cytoscape

Java

Factor_COSMOS

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

single cell RNAseq analysis of HFpEF mice model

scell_hfpef

kasumi_bench

ligrec_decouple

Systematic Comparison of Cell-Cell Communication Tools and Resources

HF_meta-analysis

Code that generates results and figures from: "A Consensus Transcriptional Landscape of Human End-Stage Heart Failure"

CKG-BioCypher

We use our tools to analysis Covid19 RNAseq datasets

Covid19

VisiumMS

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

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

CPT_QSPtutorial

Supplementary material for CPT tutorial on logic modeling for quantitative systems pharmacology

ST pipelines on mouse colon and small intestine

visium_colon_si

CNORode

add-on for CellNOptR using logic based differential equations

cyrface

Bridging Cytoscape with R

Java

FUNKI

FUNctional analysis worKflows Interface

Proteogenomics analsysis of protein attenuation in tumours

protein_attenuation

Repository to collect issues for events to be scheduled

scheduling

CellNOptR with MaBoSS simulation

CellNOptR-MaBoSS

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

Estimate tumor purities from gene expression data

cytocopter

CellNOptR in Cytoscape

Java

TumorDeconvolution

Teaching material for the single-cell course 2022

Singlecell_course_2022

ShinyCNOR

Shiny application for the CellNOptR packages

2023-SysBioCourse-ACSB

Mobi microbiome course materials

Microbiome_analysis_course_2022

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

PerMedCoE_tools_virtual_course_2023

OTAR-BioCypher

snk-tutorial

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

NicheNet_Omnipath

teaching_material

teaching material for various courses

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

process_rnaseq_cellines

TFbenchmark

This repository contains the code used to benchmark TF-target datasets via TF activities in 3 benchmark datasets

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

kinase_tf_mini_tuto_simple

Xu_tubuloid

Teaching material for 2022 SysBio Course

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

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

liver-disease-atlas-app

ccc_protocols

LIANA x Tensor-cell2cell Protocols

MOON_example

analysis and visualization workflows for the OmniPath 2 paper

omnipath_analysis

Target functional similarity based workflows for drug synergy prediction and stratification

meta_PKN_BIGG

Macau_Synergy_Prediction

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

Provisional repository for the development of CARNIVAL package for Bioconductor

CARNIVAL-Bioconductor-Dev

MedInfNetworks2021

simulator used for the Misty paper

CKD_Landscape

insilico_tissue_simulator

CNORprob

Probabilistic logic version of CellNOpt (derived from FALCON)

PHONEMeS-ILP

ILP implementation of PHONEMeS

recon3D_BIGG

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

DrugVsDisease

100

astromouse

Spatial space data from mouse