Adi Laurentiu Tarca
4 packages on Bioconductor
This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types.
This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.
This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package.
This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.