Saez Lab

progeny

R package for Pathway RespOnsive GENe activity inference

lipyd

Python module for lipidomics LC MS/MS data analysis

ocean

R package for metabolic enzyme enrichment anaylsis

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

Combi-Seq-analysis

Analysis code for Combi-Seq paper

neo4j-utils

Rich interface on top of the official Neo4j driver

ShinyCNOR

Shiny application for the CellNOptR packages

snk-tutorial

teaching_material

teaching material for various courses

2022-SysBioCourse-ACSB

Teaching material for 2022 SysBio Course

MedInfNetworks2022

OncoSignature

Scripts used to perform the analyses of OncoSignature project for AML

PHONEMeS-ILP

ILP implementation of PHONEMeS

misty_pipelines

MISTy pipelines used to generate results for the paper

Sciacovelli_Dugourd_2021_paper

code for the Sciacovelli_Dugourd_2021 manuscript

CNORfeeder

CellNOptR add-on that permits to extend a network with links derived from literature

muscat

Multi-sample multi-group scRNA-seq analysis tools

omnipath-decoupler-docker

A Docker image for teaching

plasmaContamination

plugy

Flexible processing and analysis of plug microfluidics data

pypath-cache

Cache management for directories of files.

pypath-dlmanager

Download manager for pypath

pypath-omnipath

The database builder 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.

redHuman_models

processing of the TFA constrained rehuman model based on recon 3D

saezverse

Docker image with all tools from the lab

scverse_hackathon

tum-bc