Saez Lab

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-py

Dorothea package in Python

CellNOptR

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

decoupleR_manuscript

Code to reproduce the results from decoupleR's manuscript

ligrec_decouple

Systematic Comparison of Cell-Cell Communication Tools and Resources

Combi-Seq-analysis

Analysis code for Combi-Seq paper

Microbiome_analysis_course_2022

Mobi microbiome course materials

ShinyCNOR

Shiny application for the CellNOptR packages

Singlecell_course_2022

Teaching material for the single-cell course 2022

2022-SysBioCourse-ACSB

Teaching material for 2022 SysBio Course

cell2cell

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

insilico_tissue_simulator

simulator used for the Misty paper

OncoSignature

Scripts used to perform the analyses of OncoSignature project for AML

PHONEMeS-ILP

ILP implementation of PHONEMeS

Xu_tubuloid

LogicODE_GFP_SR

LogicODE modelling of GFP reporters in stress response pathways (TransQST in collaboration with Leiden University)

marco_kidney_singlecell

mistyMBC

muscat

Multi-sample multi-group scRNA-seq analysis tools

NetworkModeling_course_2022

omnipath-decoupler-docker

A Docker image for teaching

pypath-cache

Cache management for directories of files.

pypath-dlmanager

Download manager for pypath

pypath-omnipath

The database builder part of pypath

pypath-resources

The core part of pypath.

pypath-server

A twisted based HTTP server that serves databases built by pypath.

pypath-utils

Standalone utilities that were formerly part of pypath.

saezverse

Docker image with all tools from the lab

SDOT

Supplementary code for "Spatial Cell Type Deconvolution by Optimal Transport"