Saez Lab

Julio Saez-Rodriguez's group @ EMBL-EBI and Heidelberg University

Germany

Pinned Repositories

CollecTRI
Gene regulatory network containing signed transcription factor-target gene interactions
Language:R73 7 177
decoupleR
R package to infer biological activities from omics data using a collection of methods.
Language:R235 4 10625
decoupler-py
Python package to perform enrichment analysis from omics data.
Language:Python189 5 14128
dorothea
R package to access DoRothEA's regulons
Language:R143 14 4926
liana
LIANA: a LIgand-receptor ANalysis frAmework
Language:R198 8 16933
liana-py
LIANA+: an all-in-one framework for cell-cell communication
Language:Python200 3 12725
OmnipathR
R client for the OmniPath web service
Language:R131 10 10319
progeny
R package for Pathway RespOnsive GENe activity inference
Language:R101 17 5320
pypath
Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
Language:Python139 18 20148
visium_heart
Spatial transcriptomics of heart tissue
Language:Jupyter Notebook81 2 1439

Saez Lab's Repositories

saezlab/progeny
R package for Pathway RespOnsive GENe activity inference
Language:R101 17 5320
saezlab/transcriptutorial
This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
Language:R55 8 4029
saezlab/decoupleRBench
Package to benchmark methods from decoupleR
Language:R9 3 17
saezlab/eccb2022_sc_funcomics
Functional analysis of single-cell transcriptomics
Language:HTML7 3 05
saezlab/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
Language:R3 4 03
saezlab/snk-tutorial
Language:Python2 3 0
saezlab/teaching_material
teaching material for various courses
Language:HTML2 5 02
saezlab/CNORfeeder
CellNOptR add-on that permits to extend a network with links derived from literature
Language:R1 4 11
saezlab/COSMOS_MSB
code for the COSMOS study in MSB
Language:R1 4 04
saezlab/MedInfNetworks2022
Language:HTML1 2 0
saezlab/meta_PKN_BIGG
Language:R1 3 0
saezlab/NeuralODEs
NeuralODE version of cellnopt
Language:Jupyter Notebook1
saezlab/recon3D_BIGG
Language:Jupyter Notebook1 4 0
saezlab/DREAM_HF_microbiome
Predict incident risk for heart failure in human population studies by combining fecal microbiome composition and host information
Language:R0 2 00
saezlab/misty_pipelines
MISTy pipelines used to generate results for the paper
Language:R0 4 13
saezlab/Sciacovelli_Dugourd_2021_paper
code for the Sciacovelli_Dugourd_2021 manuscript
Language:HTML0 4 00
saezlab/compclub
Computational Club materials
Language:HTML2 0
saezlab/ltp-figures
Visualizations for the LTP project
Language:Python3 0
saezlab/ltp-invitro
Processing pipeline for the in vitro LTP screen
Language:AGS Script3 0
saezlab/ltp-invivo
Processing pipeline for the in vivo LTP screen
Language:Python3 0
saezlab/orcestra_contribution
data pipelines for Orcestra
Language:R2 0
saezlab/plasmaContamination
Language:R4 0
saezlab/plugy
Flexible processing and analysis of plug microfluidics data
Language:Python3 16
saezlab/redHuman_models
processing of the TFA constrained rehuman model based on recon 3D
Language:R3 0
saezlab/RIPC_kidney
RNA-seq analysis of Kidney transplant samples
2 0
saezlab/scverse_hackathon
saezlab/Singlecell_course_2023
Language:HTML1 01
saezlab/snakemake-workshop
Language:Python3 04
saezlab/taipale_scrna-main
1 0
saezlab/tum-bc
Language:Python