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ReFACTor / Reference-Free Adjustment for Cell-Type composition

A method based on principal component analysis (PCA) and designed for the correction of cell type heterogeneity in epigenome-wide association studies (EWAS). ReFACTor tool is based on a variant of PCA and can be applied to any tissue. It selects the sites that can be reconstructed with low error using a low-rank approximation of the original methylation matrix. Moreover, ReFACTor does not use the phenotype in the selection process, making ReFACTor useful as part of a quality control step in EWAS.

RefFreeEWAS / RefFree Epigenome-Wide Association Studies

Permits reference-free deconvolution. RefFreeEWAS offers a method for evaluating the extent to which the underlying reflects specific types of cells. It differs from widely used principal components analysis (PCA)-based methods such as Surrogate Variable Analysis (SVA) in imposing biologically based constraints, thus resulting in mixture coefficients having greater biological interpretation and placing greater emphasis on coordinated cellular processes.

EDec / Epigenomic Deconvolution

Provides accurate platform-independent estimation of cell type proportions, DNA methylation profiles and gene expression profiles of constituent cell type. EDec enables deconvolution of complex tumor tissues where highly accurate reference are enables. EDec reveals layers of biological information about distinct cell types within solid tumors and about their heterotypic interactions that were previously inaccessible at such large scale due to tissue heterogeneity.


Deconvolutes of DNA methylation array data into source contributions from distinct cell types. methylSpectrum is a method for inferring changes in the distribution of white blood cells between different subpopulations using DNA methylation signatures in combination with an appropriate external validation set. methylSpectrum employs the concept of differentially methylated DNA regions (DMR) as markers of immune cell identity using a high-density methylation platform. With these considerations, a set of analytical tools for estimating the proportions of immune cells in unfractionated whole blood is proposed in methylSpectrum tool.