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@saezlab

Saez Lab

Systems Biomedicine - Julio Saez-Rodriguez's group

Welcome to the github page of Saez Lab!

We are a research group at the Institute for Computational Biomedicine at the Medical Faculty of Heidelberg University and Heidelberg University Hospital. We develop software tools for systems level analysis and mechanistic modeling of molecular and biomedical data.

Our goal is to acquire a functional understanding of the deregulation of signalling networks in disease and to apply this knowledge to develop novel therapeutics. We focus on cancer, auto-immune and fibrotic disease. Towards this goal, we integrate big (‘omics’) data with mechanistic molecular knowledge into statistical and machine learning methods. To this end, we have developed a range of tools in different areas of biomedical research, mainly using the programming languages R and Python.

Our major tools are summarized here.

Pinned

  1. pypath Public

    Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.

    Python 90 25

  2. progeny Public

    R package for Pathway RespOnsive GENe activity inference

    R 46 15

  3. CARNIVAL Public

    CAusal Reasoning for Network Identification with integer VALue programming in R

    R 38 24

  4. dorothea Public

    R package to access DoRothEA's regulons

    R 73 21

  5. liana Public

    LIANA: a LIgand-receptor ANalysis frAmework

    R 40 3

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

    Python 13 4

Repositories

  • plugy Public

    Flexible processing and analysis of plug microfluidics data

    Python 0 GPL-3.0 0 0 0 Updated May 16, 2022
  • liana Public

    LIANA: a LIgand-receptor ANalysis frAmework

    R 40 GPL-3.0 3 2 0 Updated May 13, 2022
  • Singlecell_course_2022 Public

    Teaching material for the single-cell course 2022

    0 GPL-3.0 0 0 0 Updated May 12, 2022
  • CRCDiet Public

    CRCDiet

    Jupyter Notebook 0 MIT 0 0 0 Updated May 12, 2022
  • Microbiome_analysis_course_2022 Public

    Mobi microbiome course materials

    HTML 0 0 0 0 Updated May 12, 2022
  • CellNOptR Public

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

    R 6 2 2 1 Updated May 11, 2022
  • CNORfeeder Public

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

    R 0 1 1 0 Updated May 11, 2022
  • mistyR Public

    Multiview Intercellular SpaTial modeling framework

    R 11 GPL-3.0 6 1 1 Updated May 10, 2022
  • pypath Public

    Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.

    Python 90 GPL-3.0 25 13 (3 issues need help) 0 Updated May 9, 2022
  • decoupleR Public

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

    R 39 GPL-3.0 11 0 0 Updated May 9, 2022