Rmagpie

Statistic methods to evaluate variations of differential expression (DE) between multiple biological conditions. It takes into account the fold-changes and p-values from previous differential expression (DE) results that use large-scale data (*e.g.*, microarray and RNA-seq) and evaluates which genes would react in response to the distinct experiments. This evaluation involves an unique pipeline of statistical methods, including weighted summarization, quantile detection, cluster analysis, and ANOVA tests, in order to classify a subset of relevant genes whose DE is similar or dependent to certain biological factors.

Implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis and differential expression analysis.

Tools for export and import classification trees and clusters to other programs

Pigengene package provides an efficient way to infer biological signatures from gene expression profiles. The signatures are independent from the underlying platform, e.g., the input can be microarray or RNA Seq data. It can even infer the signatures using data from one platform, and evaluate them on the other. Pigengene identifies the modules (clusters) of highly coexpressed genes using coexpression network analysis, summarizes the biological information of each module in an eigengene, learns a Bayesian network that models the probabilistic dependencies between modules, and builds a decision tree based on the expression of eigengenes.

This packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input.

Tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided.