This page contains some of the software used in the implementation
my recent publications. More software is available from the PUMA webpage.
PPCA: a matlab package containing the code and demos used in
"Accounting for Probe-level Noise in the Processing of Microarray Data
with Principal Component Analysis", G.S., Marta Milo, Magnus Rattray
and Neil D. Lawrence (also available in R from PUMA).
Unsupervised LDA, a matlab package containing an
implementation of the model described in my recent paper "Dimensionality
reduction of clustered data sets" (to appear in IEEE TPAMI)
MMG, a matlab package for a finding submodules of
metabolic networks, as described in this Bioinformatics paper.
swRegVariational and swRegExact a matlab and C packages for inferring
TF reaction to stress bioinformatics paper.
multiSwitch a MATLAB package for combinatorial regulation, described in Opper and Sanguinetti, Bioinformatics 26(13), 2010. A brief documentation can be found here
TFInfer an open-source package extending and optimising the method described in Sanguinetti et al, Bioinformatics 22(22):2775-2781 (2006). An application note describing the software has appeared in Asif et al, Bioinformatics 26(20), 2010.
Multi-task GP classification (method under
review), a demo of the MATLAB code developed by Grigorios Skolidis. You will need some extra files which can be
publicly downloaded, see instructions in README.txt.
Large scale inference of combinatorial regulation, MATLAB package developed by Shahzad Asif implementing the work described in this Bioinformatics paper.
Inference in hierarchical networks, MATLAB package developed by Andrea Ocone implementing the work described in this Bioinformatics paper.
Testing chip-seq histograms developed by Gabriele Schweikert journal link.
Hybrid Regulatory Models developed by Andrea Ocone journal link.
Multi-task GP regression for inference of pKA developed by Grigorios Skolidis for the paper Multi-task learning for pKa prediction, Skolidis, Hansen, Sanguinetti and Rupp, in press with Journal of Computer Aided Molecular Design.
DSS, network inference for oscillatory networks, developed by Daniel Trejo-Banos (paper under review).
MDC, modular differential connection modelling, developed by Ronald Begg (paper under review)