EWAS Toolkit

EWAS Toolkit @ EWAS Open Platform
a web toolkit for epigenome-wide association study

Analyze with Local IDAT & Metadata Files
Analyze with Public Project ID

Local Input

Input IDAT files *

No archive selected

IDAT

Input MetaData files *

No metadata file selected

Metadata

Parse uploaded files & load sample summary panel

Public Dataset Input

Analyze with Public Project ID *

Support one or more public dataset Project IDs; samples will be loaded from EWAS Data Hub repository.

Selected Sample Summary

samples loaded from your input

Selected Samples

Array Type

Project ID

Submit a data source to load metadata traits.

Analysis Configuration

Submit files or Project ID first. Step 1-4 will be enabled after metadata is loaded.

Step 1/4 Basic Settingsanalysis name, scope & description

Task Name (Optional)

A timestamp (_YYYYMMDD_HHMMSS_fff) is appended automatically on submission.

Analysis Scope*

DMP: Differentially Methylated PositionDefault DMR: Differentially Methylated Region

Description (Optional)

Step 2/4 Group & Contrast Settingsarray type & case / control groups

Select Trait*

Trait Type

Methylation Array Type*

Step 3/4 Confounder Correctionquality control & covariate adjustment

Pre-filter Settings (Quality Control)

Filter low-quality probes (Detection p > 0.05) Remove sex chromosome probes Filter probes with low call rate [%]

Selected Covariates (Confounders) (Optional)

Step 4/4 Statistical Methods & Thresholdsp-value & effect size cutoffs

Significance Thresholds

P-value cutoff Adjusted P-value cutoff (Optional)

Effect Size

Methylation Δβ cutoff (Optional)

DMR Parameters

Window size bp

Minimum probes per region

Input Job ID

More details about EWAS Toolkit can be found at Documentation Page.
If you use EWAS Toolkit, please cite: EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study. Nucleic Acids Res. 2021. doi:10.1093/nar/gkab972. [PMID=34718752]

EWAS Toolkit @ EWAS Open Platform a web toolkit for epigenome-wide association study

Selected Sample Summary

More details about EWAS Toolkit can be found at Documentation Page. If you use EWAS Toolkit, please cite: EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study. Nucleic Acids Res. 2021. doi:10.1093/nar/gkab972. [PMID=34718752]

EWAS Toolkit @ EWAS Open Platform
a web toolkit for epigenome-wide association study

More details about EWAS Toolkit can be found at Documentation Page.
If you use EWAS Toolkit, please cite: EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study. Nucleic Acids Res. 2021. doi:10.1093/nar/gkab972. [PMID=34718752]