Saez-Rodriguez Group

BioServices is a Python package that provides access to many Bioinformatics Web Services (e.g., UniProt) and a framework to easily implement Web Service wrappers (based on WSDL/SOAP or REST protocols).

Birewire is an R package implementing high-performing routines for the randomisation of bipartite graphs preserving their node degrees (i.e. Network Rewiring), through the Switching Algorithm (SA) . BiRewire analytically estimates the number of Switching Steps to be performed in order for the similarity between the original network and its rewired version to reach a plateau (i.e. to achieve the maximal level of randomness) according to the lower bound.

Cyrface establishes an interface between R and Cytoscape by using different Java-R libraries, e.g. Rserve, RCaller. Cyrface can be used as a Cytos cape plug-in, e.g. to run R commands within Cytoscape, or used as a library to allow your plug-in to connect to R.

CySBGN is a Cytoscape plug-in that extends the use of Cytoscape visualization and analysis features to SBGN maps. CySBGN adds support to Cytoscape to import, export, visualize, validate and analyse SBGN maps.

DREAMTools provides the code used in the scoring of DREAM challenges that pose fundamental questions about system biology and translational medicine.

DrugVsDisease (DvD) provides a pipeline, available through R or Cytoscape, for the comparison of drug and disease gene expression profiles from public microarray repositories.

GDSCTools is an open-source Python library dedicated to the study pharmacogenomic relationships in the context of the GDSC (Genomics of Drug Sensitivity in Cancer) project. The main developer is Thomas Cokelaer (Institut Pasteur), and it is a joint effort with the groups of Mathew Garnett (Sanger Institute) and Julio Saez-Rodriguez.

GDSCTools is hosted by  GitHub and documented here.

iNRG_cMap (iterative NetwoRk Guided connectivity Mapping) a strategy that refines these unbiased approaches by making use of prior knowledge about the analysed compounds to compute refined transcriptional signatures of drug response. Making use of transcriptional data from the Connectivity Map and building on the MANTRA method, iNRG_cMap is able to disentangle spurious effects due to non-relevant secondary drug effects, thus enhancing the predictive power of the resulting refined signatures.

KinAct is a python package with different computational methods to infer kinase activities from phosphoproteomics datasets.

MEIGO is a global optimization toolbox that includes a number of metaheuristic methods as well as a Bayesian inference method for parameter estimation. It is developed jointly with the group of Julio Banga.

MEIGO is described in (Egea et al, BMC Bioinformatics, 2014), and hosted here.

SLAPEnrich, a statistical method implemented in an open source R package, to identify pathway-level enrichments of genetic alterations.