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EWAS software tools and databases

The goal of epigenome-wide association studies (EWAS), analogous to that of genome-wide association studies (GWAS), is to identify changes in the epigenome at particular loci that are correlated with a phenotype of interest.Source text:(Zou et al.,…
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…

eFORGE
Web
Desktop
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…

GLINT
Desktop

GLINT

Allows fast analysis of genome-wide DNA methylation data generated using the…

Allows fast analysis of genome-wide DNA methylation data generated using the Illumina human methylation arrays. GLINT allows to easily run a pipeline of Epigenome-Wide Association Study (EWAS) under…

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…

CpGFilter
Desktop

CpGFilter

Filter CpGs based on intra-class correlation coefficients (ICCs) when…

Filter CpGs based on intra-class correlation coefficients (ICCs) when replicates are available. ICCs are calculated by fitting linear mixed effects models to all samples including the un-replicated…

GEM
Desktop

GEM Gene Environment and Methylation

Explores the associations of Gene, Environment and Methylation. GEM offers…

Explores the associations of Gene, Environment and Methylation. GEM offers linear regression models to facilitate analyses in epigenome wide association studies (EWAS). It permits users to test…

QCEWAS
Desktop

QCEWAS

Enables automated quality control of results files of epigenome-wide…

Enables automated quality control of results files of epigenome-wide association studies (EWAS). QCEWAS produces cohort-specific statistics and graphs to interpret the quality of the results files,…

BayesCCE
Desktop

BayesCCE Bayesian Cell Count Estimation

Encodes experimentally obtained cell count information as a prior on the…

Encodes experimentally obtained cell count information as a prior on the distribution of the cell type composition in the data. BayesCCE is a Bayesian semi-supervised method that leverages prior…

EDec
Desktop

EDec Epigenomic Deconvolution

Provides accurate platform-independent estimation of cell type proportions, DNA…

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…

SmartSVA
Desktop

SmartSVA

Captures variation of unknown sources for high-dimensional data sets. SmartSVA…

Captures variation of unknown sources for high-dimensional data sets. SmartSVA is based on a surrogate variable analysis (SVA) method that protects the signals when capturing the cell mixtures. The…

EpiDISH
Desktop

EpiDISH Epigenetic Dissection of Intra-Sample Heterogeneity

Uses DNAse Hypersensitive Site (DHS) data from the NIH Roadmap and ENCODE to…

Uses DNAse Hypersensitive Site (DHS) data from the NIH Roadmap and ENCODE to construct a reference DNAm database. EpiDISH is a reference-based algorithm, for in-silico deconvolution of DNA…

EWAS
Desktop

EWAS Epigenome-Wide Association study Software

Identifies the disease-related methylecomtypes. EWAS is based on the framework…

Identifies the disease-related methylecomtypes. EWAS is based on the framework of haplotype-based association study in Haploview extended to DNA methylation data. The tool can (1) calculate the DNA…

coMET
Desktop
Web

coMET

A web-based plotting tool and R-based package to visualize EWAS (epigenome-wide…

A web-based plotting tool and R-based package to visualize EWAS (epigenome-wide association scan) results in a genomic region of interest. coMET provides a plot of the EWAS association signal and…

NEpiC
Desktop
MethylPCA
Desktop

MethylPCA

Provides users a convenient tool to perform methylome-wide association studies…

Provides users a convenient tool to perform methylome-wide association studies (MWAS). The software effectively handles the challenge in memory and speed to perform tasks that would be impossible to…

BECon
Web

BECon Blood-Brain Epigenetic Concordance

Provides a resource to the community to aid interpretation of blood based DNA…

Provides a resource to the community to aid interpretation of blood based DNA methylation results in the context of brain tissue. BECon provides metrics data on: the variability of CpGs in blood and…

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