Greenwood Lab Statistical Genetics at the Lady Davis Institute

Software

funtooNorm

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

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

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

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


Eclust

This software is written in the open source software environment R. It’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.


CellTypeAdjustment

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