Discover saezlab/FootprintMethods_on_scRNAseq Open Source project

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

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

footprints

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

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

CellNOptR

SLAPenrich

Sample Level Analysis of Pathway Alteration Enrichments

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