ROTS R-package implements the reproducibility-optimized test statistic (ROTS) for ranking genes or proteins in terms of differential expression in two-group comparisons.

DCeN R-package implements the Dynamically Co-expressed Neighborhoods (DCeN) for ranking genes in genome-wide time-resolved gene expression profiling studies.

PECA R-package implements Probe/peptide-level Expression Change Averages (PECA) for improved differential expression analysis for Affymetrix microarrays and proteomics.

PASI Pathway analysis tool implements Pathway Analysis for Sample-level Information (PASI) that provides pathway values for each analyzed sample and pathway separately.

Phosphonormalizer R-package compensates for the bias introduced by median normalization in phosphoproteomics.

SimPhospho Proteomics software for simulation of spectra of phosphopeptides enabling confident phosphosite assignment.

CETEG R package implements the CEll Type Extractor for Gene expression (CETEG) for detecting the cell type specific expression profiles from bulk gene expression data.

LC R-program implements a robust (longitudinal) binary classification method called Likelihood Contrasts (LC).