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Login

You need an username and password in order to login the MethPanel shinyApp. After login, you can choose which project to work on, you can also logout here.

1. FASTQ QC

The trimmed FASTQ metrics table are displayed on the right-hand side. For further examination, you can select any sample at the sidebar and click the Download button to download details of these metrics.

2. Alignment

You can select any metric to visualize here, the rest of metrics that cannot be plotted are also shown in table.

3. DNA methylation

The DNA methylation tab including 3 pages as follow:

Overview

You can visualize heatmaps for coverage and DNA methylation ratio here, simply choose which option to display on the left-hand sidebar

Amplicon DNA methylation

boxplots for all amplicons and single amplicon

DNA methylation for group

After downloading the template, the Group column need to be filled in.

where users can visualise amplicon in group for comparison

4. Pattern

Pattern of DNA methylation can be shown in the heatmaps.

5. Polymorphism

Polymorphism scores can be plotted for all amplicons and single amplicon.

6. PCR bias correction

After downloading the template, the Expectation column (of DNA methylation from spike-in samples) need to be filled in.

MethPanel allows users to correct PCR bias by amplicon and CpG site. The full table of before and after DNA methylation can be downloaded.