saezlab/ShinyFUNKI

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R
License
GNU Affero Genera...
Created about 6 years ago
Updated almost 3 years ago

saezlab/ShinyFUNKI

saezlab

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

decoupleR

R package to infer biological activities from omics data using a collection of methods.

liana

LIANA: a LIgand-receptor ANalysis frAmework

decoupler-py

Python package to perform enrichment analysis from omics data.

liana-py

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

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 regulons

OmnipathR

R client for the OmniPath web service

progeny

R package for Pathway RespOnsive GENe activity inference

visium_heart

Spatial transcriptomics of heart tissue

Jupyter Notebook

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.

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

FootprintMethods_on_scRNAseq

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

footprints

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

corneto

Unified knowledge-driven network inference from omics data

lipyd

Python module for lipidomics LC MS/MS data analysis

flop

FunctionaL Omics Processing platform

progeny-py

PROGENY Python implementation

Jupyter Notebook

dorothea-py

Dorothea package in Python

Jupyter Notebook

MOFAcell

Code used for muti cellular factor analysis

Jupyter Notebook

ocean

R package for metabolic enzyme enrichment anaylsis

kinact

Toolbox for Kinase Activity Scoring based on phosphoproteomic data

BioCypher

A unified language for biomedical research knowledge graphs

CellNOptR

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

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.

decoupleR_manuscript

Code to reproduce the results from decoupleR's manuscript

eccb2022_sc_funcomics

Functional analysis of single-cell transcriptomics

PHONEMeS

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

Omnipath_Cytoscape

a plug-in to access Omnipath from Cytoscape

Factor_COSMOS

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

scell_hfpef

single cell RNAseq analysis of HFpEF mice model

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

Covid19

We use our tools to analysis Covid19 RNAseq datasets

VisiumMS

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

PerMedCoE_summer_school_2023

PerMedCoE summer school 2023

Jupyter Notebook

cellnopt

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

CPT_QSPtutorial

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

visium_colon_si

ST pipelines on mouse colon and small intestine

CNORode

add-on for CellNOptR using logic based differential equations

cyrface

Bridging Cytoscape with R

FUNKI

FUNctional analysis worKflows Interface

protein_attenuation

Proteogenomics analsysis of protein attenuation in tumours

scheduling

Repository to collect issues for events to be scheduled

CellNOptR-MaBoSS

CellNOptR with MaBoSS simulation

CNORode2017

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

liverx

Analysis of liver proteomics data from Aebersold lab

neo4j-utils

Rich interface on top of the official Neo4j driver

cytocopter

CellNOptR in Cytoscape

TumorDeconvolution

Estimate tumor purities from gene expression data

Singlecell_course_2022

Teaching material for the single-cell course 2022

ShinyCNOR

Shiny application for the CellNOptR packages

2023-SysBioCourse-ACSB

Microbiome_analysis_course_2022

Mobi microbiome course materials

PerMedCoE_tools_virtual_course_2023

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

Jupyter Notebook

OTAR-BioCypher

snk-tutorial

NicheNet_Omnipath

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

teaching_material

teaching material for various courses

process_rnaseq_cellines

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

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".

Jupyter Notebook

kinase_tf_mini_tuto

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_simple

Xu_tubuloid

2022-SysBioCourse-ACSB

Teaching material for 2022 SysBio Course

NetworkModeling_course_2020

teaching materials for the network modeling course

gene-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

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

Jupyter Notebook

MOON_example

omnipath_analysis

analysis and visualization workflows for the OmniPath 2 paper

meta_PKN_BIGG

Macau_Synergy_Prediction

Target functional similarity based workflows for drug synergy prediction and stratification

MedInfNetworks2022

breastCancerCytof

modelling breast cancer cytof data with logic ODEs

BiRewire

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 microenvironment

network_tools

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

Jupyter Notebook

Meta_PKN

integration of omnipath causal network with STITCH and Recon3D

biocypher-project-template

Template for creating a BioCypher-driven knowledge graph

CARNIVAL-Bioconductor-Dev

Provisional repository for the development of CARNIVAL package for Bioconductor

MedInfNetworks2021

CKD_Landscape

insilico_tissue_simulator

simulator used for the Misty paper

CNORprob

Probabilistic logic version of CellNOpt (derived from FALCON)

PHONEMeS-ILP

ILP implementation of PHONEMeS

recon3D_BIGG

Jupyter Notebook

DrugVsDisease

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

astromouse

Spatial space data from mouse

Jupyter Notebook