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 allows improved differential expression analysis for Affymetrix microarrays and proteomics studies and is based on Probe/peptide-level Expression Change Averages
PASI Pathway Analysis for Sample-level Information
Phosphonormalizer uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.
SimPhospho Proteomics software for simulation of spectra of phosphopeptides