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Cell composition correction software tools | DNA methylation microarray data analysis

Whole blood is frequently utilized in genome-wide association studies of DNA methylation patterns in relation to environmental exposures or clinical outcomes. However, for DNA methylation assessed from whole blood, the association between DNA…
RnBeads
Desktop

RnBeads

An R package for comprehensive analysis of DNA methylation data obtained with…

An R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution, including Infinium 450K microarray and bisulfite…

ReFACTor
Desktop

ReFACTor Reference-Free Adjustment for Cell-Type composition

A method based on principal component analysis (PCA) and designed for the…

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…

ChAMP
Desktop

ChAMP

Allows Illumina HumanMethylation BeadChip analysis. ChAMP is an integrated…

Allows Illumina HumanMethylation BeadChip analysis. ChAMP is an integrated analysis pipeline including functions for (i) filtering low quality probes, adjustment for Infinium I and Infinium II probe…

minfi
Desktop

minfi

A suite of computational tools that incorporate state-of-the-art statistical…

A suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data. minfi provides methods for preprocessing, quality assessment and detection of…

FaST-LMM-EWAShe…
Desktop

FaST-LMM-EWASher

An R version of FaST-LMM-EWASher, which performs epigenome-wide association…

An R version of FaST-LMM-EWASher, which performs epigenome-wide association analysis in the presence of confounders such as cell-type heterogeneity. A python version of this software is also…

RefFreeEWAS
Desktop

RefFreeEWAS RefFree Epigenome-Wide Association Studies

Permits reference-free deconvolution. RefFreeEWAS offers a method for…

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…

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