Pinned Repositories
CollecTRI
Gene regulatory network containing signed transcription factor-target gene interactions
decoupleR
R package to infer biological activities from omics data using a collection of methods.
decoupler-py
Python package to perform enrichment analysis from omics data.
dorothea
R package to access DoRothEA's regulons
liana
LIANA: a LIgand-receptor ANalysis frAmework
liana-py
LIANA+: an all-in-one framework for cell-cell communication
OmnipathR
R client for the OmniPath web service
progeny
R package for Pathway RespOnsive GENe activity inference
pypath
Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
visium_heart
Spatial transcriptomics of heart tissue
Saez Lab's Repositories
saezlab/CPT_QSPtutorial
Supplementary material for CPT tutorial on logic modeling for quantitative systems pharmacology
saezlab/protein_attenuation
Proteogenomics analsysis of protein attenuation in tumours
saezlab/liverx
Analysis of liver proteomics data from Aebersold lab
saezlab/BiRewire
An R package implementing high-performing routines for the randomisation of bipartite graphs preserving their node degrees.
saezlab/DrugVsDisease
DvD: An R and Cytoscape plug-in for comparing Drug and Disease profiles
saezlab/yeast_phospho
Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast
saezlab/cysbgn
saezlab/ebits
R modules for common tasks
saezlab/hlrcc
Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells
saezlab/iNRG_cMAP
Iterative Network Guided Connectivity Mapping http://www.ebi.ac.uk/~iorio/PLoS_ONE_Submission
saezlab/Sciacovelli_et_al
Code of paper Sciacovelli et al. Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition, Nature, 2016