The R package funtooNorm provides a function for normalization of Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K) data when there are samples from multiple tissues or cell types.

pcev is an R package which implements Principal components of explained variance (PCEV); it is a statistical tool which be used for the analysis of a mutivariate response vector. It is a dimension-reduction technique, similar to Principal components Analysis (PCA), which seeks to maximize the proportion of variance (in the response vector) being explained by a set of covariates. Stable release on CRAN

RVPedigree is an R package which is a collection of the five region-based rare-variant genetic association tests. The following tests are currently implemented: ASKAT, ASKAT-Normalized, VC-C1, VC-C2 and VC-C3.

MURAT is an R package to conduct rare-variant association tests for multiple continuous traits

This software is written in the open source software environment R. Itâ€™s main functionality is to fit statistical models for analyzing interactions between a high dimensional dataset (e.g. genomics, brain imaging), the environment and a response. It automatically performs variable selection and estimation, while conserving the strong heredity property, i.e., an interaction term is selected only if the main effects are in the model.

R script showing examples of running methods adjusting for cell type composition in DNA methylation studies (450K). Simulated data is available as well: https://zenodo.org/record/46746#.VtW7MmSAOko