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thinhong edited this page Oct 28, 2020 · 6 revisions

Install shiny server

This is an installation manual for Ubuntu server.

  1. Edit file /etc/apt/sources.list on the server to include the latest link to update CRAN:
sudo nano /etc/apt/sources.list

Manually check your Ubuntu version using lsb_release -a to decide which link should be inserted, for example, this is a link for Ubuntu 18.04 bionic:

deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/

Press Ctrl+O > Enter to save the file, then press Ctrl+X to exit nano editor.

  1. Update apt and install R
sudo apt-get update

During updating some machines will report errors such as missing key 51716619E084DAB9, to obtain the key please use:

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 51716619E084DAB9

Then update again and install R

sudo apt-get update
sudo apt-get install r-base
  1. Install shiny server following guidance from https://rstudio.com/products/shiny/download-server/ubuntu/ 
sudo su - \
-c "R -e \"install.packages('shiny', repos='https://cran.rstudio.com/')\""
sudo apt-get install gdebi-core
wget https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.13.944-amd64.deb
sudo gdebi shiny-server-1.5.13.944-amd64.deb

ShinyApp structure on shiny server

After installing shiny server, download file app.R and folder www on this GitHub and put it into /srv/shiny-server/MethPanel with a structure as follows:

/srv/shiny-server/MethPanel
    |-- app.R
    |-- www
        |-- full_read.png

Link essential outputs from upstream analysis to shiny server

Edit file /srv/shiny-server/MethPanel/app.R (file app.R on this GitHub) as follows:

  • Edit /path/to/upstream/analysis to match your upstream analysis folder
  • Manually create password for each user, username must be the same as the /path/to/upstream/analysis/<user>

shinyApp features

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

Login page: You are required to login with your username and password here for secure sharing data with your collaborators.

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

2. Alignment: You can select any alignment metric to visualize here and download a table comprised 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. Epipolymorphism: The relationship between epipolymorphism 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.

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