DESCRIPTION

Package: methylaction
Maintainer: Jeffrey Bhasin <jeffb@case.edu>
Author: Jeffrey Bhasin <jeffb@case.edu>
Version: 2.0
License: MIT
Title: MethylAction: Differentially Methylated Regions (DMRs) from MBD-isolated
    Genome Sequencing (MiGS/MBD-seq)
Description: Performs a two-stage testing approach on non-overlapping windows
    genome-wide to detect differentially methylated regions (DMRs). The statistical DMRs called by differences in group means are then divided into "frequent" and "other" DMRs to aid in interpretation. Multi-group statistical testing is handled with an analysis of deviance (ANODEV) approach using the GLM functionality of DESeq. Provides functions for bootstrapping the entire method to establish false discovery rates (FDRs).
Depends:
    data.table,
    GenomicRanges,
    IRanges,
    DESeq,
    goldmine
Imports:
    parallel,
    RColorBrewer,
    DESeq,
    GenomicAlignments,
    Repitools,
    reshape,
    Rsubread,
    R.utils