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Overview

The shinyApp client of MethPanel consists of a login page and 7 tabs:

Login page: You are required to login with your username and password here.

1. Trimmed FASTQ QC: You can view quality control metrics and download quality control report of your concerned sample or all samples here.

2. Alignment: You can select any alignment metric to visualize here and download a table comprises of all metrics. You can also annotate the groups of your samples and visualize these metrics by group.

3. DNA methylation: This tab allows you to discover DNA methylation levels of your samples and amplicons with a variety of options. You can also annotate the groups of your samples and make comparison among your groups, p-value of two-sided t test are provided.

4. Pattern: The pattern of amplicons are displayed here, you are free to zoom in the interactive plots to investigate them in more details.

5. Polymorphism: The relationship between polymorphism score and methylation level is plotted here.

6. PCR bias correction: MethPanel allows you to perform PCR bias correction if your experiment was conducted with control spike-in samples. The correction can be performed on amplicon or CpG site resolution.

7. DNA methylation after correction: This tab has the same content as tab 3. DNA methylation, except that the DNA methylation levels here are corrected with the tool in tab 6. PCR bias correction.