| EWAS Tools Suite includes raw intensity data loading .idat preprocessing, optional normalisation of the data, quality control with additional sample check. It gives the user the opportunity to perform any of these preparation and data cleaning steps, including the next highly recommended genetic variation annotation step resulting in single nucleotide polymorphism identification and removal by simply running the tools. Finally, the dataset generated through all of these steps can be used to hunt find differentially-methylated positions DMP and regions DMR with respect to a phenotype co-variate. |
hg clone https://toolshed.g2.bx.psu.edu/repos/kpbioteam/ewastools
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| to find differentially methylated positions | 1.28.0 | 16.01 | |
| to find differentially methylated regions | 1.28.0 | 16.01 | |
| drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension | 1.28.0 | 16.01 | |
| obtain Beta value matrix | 1.28.0 | 16.01 | |
| get the coordinating node associated with this D1Client object | 1.28.0 | 16.01 | |
| returns the Fisher information corresponding to a model and a design | 1.28.0 | 16.01 | |
| retrieve the chromosome and the position of each SNP | 1.28.0 | 16.01 | |
| mapping Ilumina methylation array data to the genome | 1.28.0 | 16.01 | |
| Create objects contains CpGs signals | 1.28.0 | 16.01 | |
| implements the functional normalization algorithm | 1.28.0 | 16.01 | |
| implements stratified quantile normalization preprocessing | 1.28.0 | 16.01 | |
| provides a simple quality control matrix and plot | 1.28.0 | 16.01 | |
| load .IDAT files | 2.1.0 | 16.01 | |
| store Beta values and/or M values | 1.28.0 | 16.01 | |