Bayesian Non-negative matrix algorithm. Used for pattern identification algorithm from genomics data. Implemented in the R/Bioconductor package CoGAPS.
EVA compares the dissimilarity between genomic profiles in sample groups. EVA can be applied for pathway dysregulation and splice variation. EVA is implemented in the R/Bioconductor package GSReg, along with the permutation-based DIRAC algorithm.
The CancerInSilico R/Bioconductor package implements a mathematical model of cellular growth in R.
pSVA removes technical artifacts in known batches from high-throughput data while preserving inter-sample heterogeneity for machine learning and unsupervised analysis. The algorithm is implemented in the R/Bioconductor package SVA.