@saezlab

Saez Lab

Systems Biomedicine - Julio Saez-Rodriguez's group

Pinned repositories

  1. CellNOptR_packages_archived

    Forked from cellnopt/CellNOptR

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

    C

  2. pypath

    python module for signaling pathways analysis accompanying OmniPath

    Python 22 14

  3. bioservices

    a Python package that provides access to many Bioinformatices Web Services

  4. SLAPenrich

    Sample Level Analysis of Pathway Alteration Enrichments

    R 5 1

  5. cytocopter

    CellNOptR in Cytoscape

    Java 1

  6. PHONEMeS

    PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is an R package to model signalling networks based on untargeted phosphoproteomics

    R 2 2

  • python module for signaling pathways analysis accompanying OmniPath

    Python 22 14 GPL-3.0 Updated Oct 18, 2018
  • Cell-type specific parameters of signalling pathway models as biomarkers for drug sensitivity

    R 2 GPL-3.0 Updated Oct 15, 2018
  • Collection of Python functions and classes designed to make data scientists' life easier.

    Python 2 GPL-3.0 Updated Oct 11, 2018
  • Target functional similarity based workflows for drug synergy prediction and patient stratification

    R Updated Oct 7, 2018
  • Linking drug target and pathway activation for effective therapy using multi-task learning

    R 2 1 GPL-3.0 Updated Oct 2, 2018
  • Discriminant Regulon Enrichment Analysis. A set of tools to compute individual TF activities

    R 4 3 GPL-2.0 Updated Sep 15, 2018
  • Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.

    R 2 Updated Aug 23, 2018
  • add-on for CellNOptR using logic based differential equations

    C 1 GPL-3.0 Updated Aug 22, 2018
  • A general purpose Python module for processing Full Moon Biotech PEX100 phosphoassay data and many other scripts for its further analysis in Pellegrinelli et al 2018

    Python Updated Aug 3, 2018
  • BraDiPluS (Braille Display Plugs Data Analysis) is an R package to process and analyse data produced using the microfluidic platform for functional drug screening of patient biopsies developed in collaboration with Merten group (EMBL).

    R 2 GPL-3.0 Updated Jul 12, 2018
  • R Updated Jun 11, 2018
  • R package for Pathway RespOnsive GENe activity inference

    R 3 2 Apache-2.0 Updated May 24, 2018
  • Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"

    R 3 3 GPL-3.0 Updated May 11, 2018
  • an extension of CellNOptR that allows to train a Boolean model agains time-courses of data.

    R Updated Apr 19, 2018
  • CellNOptR in Cytoscape

    Java 1 Updated Apr 9, 2018
  • CellNOptR extension using constrained fuzzy logic

    R Updated Jan 11, 2018
  • CellNOptR add-on that permits to extend a network with links derived from literature

    R Updated Jan 10, 2018
  • Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.

    C 2 Updated Jan 9, 2018
  • modified version of CNORode including: steady state penalty, L1 regularisation, bootstrap, new transfer function

    C 2 GPL-3.0 Updated Nov 16, 2017
  • CellNOptR with MaBoSS simulation

    R 1 1 Updated Oct 25, 2017
  • Toolbox for Kinase Activity Scoring based on phosphoproteomic data

    Python GPL-3.0 Updated Oct 20, 2017
  • E Updated Sep 29, 2017
  • Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells

    HTML GPL-3.0 Updated Jun 14, 2017
  • Proteogenomics analsysis of protein attenuation in tumours

    Python 2 GPL-3.0 Updated Jun 13, 2017
  • Tool for training of logic models of signalling networks using prior knowledge networks and perturbation data.

    Updated Jun 1, 2017
  • DvD: An R and Cytoscape plug-in for comparing Drug and Disease profiles

    R GPL-3.0 Updated May 31, 2017
  • Supplementary material for CPT tutorial on logic modeling for quantitative systems pharmacology

    Python GPL-3.0 Updated May 29, 2017
  • An R package implementing high-performing routines for the randomisation of bipartite graphs preserving their node degrees.

    1 GPL-3.0 Updated May 3, 2017
  • PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is an R package to model signalling networks based on untargeted phosphoproteomics

    R 2 2 GPL-2.0 Updated May 3, 2017
  • Bridging Cytoscape with R

    Java 2 1 Updated May 2, 2017
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