An R/Shiny dashboard to map and visualize cytosine-guanine (CG/CpG) dinucleotides and microarray-targeted probes.
To cite this tool, you may use the following:
"cgmappeR". GitHub repository. Sean Maden. 2024.
It is fast and easy to set up and run cgmappeR. This section details how.
Clone the latest version of cgmappeR from your terminal with:
git clone https://github.com/metamaden/cgmappeR"
Now install all dependencies by calling the script cgmapper/inst/r/install.R:
R ./inst/install.R
This installs dependencies from CRAN and Bioconductor. These include shiny, shinythemes, shinyWidgets, devtools, Gviz, BSgenome.Hsapiens.UCSC.hg19, org.Hs.eg.db, and TxDb.Hsapiens.UCSC.hg19.knownGene.
Run the dashboard from shell with:
Rscript ./cgmappeR/inst/run.R
The cgmappeR UI is reactive to user input, and will start with no input. Specify inputs such as the coordinate ranges and your input data using the menu options to the left.
Iteratively map CG dinucleotides and Illumina CpG probe locations in genome ideograms.
Enter a valid gene symbol, load its coordinates, and modify coordinates for the ideogram window.
Using dropdown menus, select tracks to visualize and fine tune image dimensions. Optionally add a custom cursor using custom coordinates. (Note: CpG tracks are only shown if CpGs overlap with view window)
Click View Genome button to load the genome ideogram at the indicated coordinates.
View resultant ideogram (first tab), CG dinucleotide table (second tab), CpG probe annotations table (third tab), and/or sequence in the selected window (fourth tab).
The lefthand menu contains filter, query, import, and export options.
The different tabs will switch the display between complementary information for a specified view window, including ideogram plot, dinucleotide coordinates table, probe annotations, and genome sequence.
View Ideogram Tab:
View CG Dinucleotides Table Tab:
View CpG Probes Table Tab:
View Sequence Tab:
Use the coordinates and other filters at the lefthand menu in order to modify the view window, such as shift upstream, downstream, expand the view window, or narrow the view window.
You may view your own probe data in the cgmappeR ideogram by selecting from the left menu.
You may save the probe annotations, dinucleotide coordinates, and sequence using the bottom-left menu options.
Download the image by right-clicking, and download the tables using the download buttons.
