Newbie - Plotting Genes on Genomic Axis and Creating a Genomic Browser

Question

[berrysweetpie]

I have genomic data involving multiple genes of Yeast and wish to create a Genomic Browser with several tracks with Shiny and R. I would like to incorporate statistical analysis on transcription width for each gene below it.

At the very least, I wish to be able to plot all the genes with a name label on the genomic axis.

Any packages that can be used to do this?

[cyril-cros]

If I may, reinventing the wheel is a waste of time - unless you are doing it as a personal project. https://www.broadinstitute.org/igv/ is always nice, and there is also the UCSC genome browser - they can at least give you an idea of what functionalities to implement.

[berrysweetpie]

That makes sense, thank you. Will these include functionality to add custom tracks with statistics?

[dandan]

Yep, it's very easy and fast to add custom tracks to UCSC with .bed files. Please see https://genome.ucsc.edu/goldenPath/help/customTrack.html for more information.

[berrysweetpie]

Awesome, thanks for all your help!

[dandan]

(sorry duplicate post)

Answer 1

[Asaf]

You can use Gviz, an example can be found in:

https://github.com/Bioconductor/CSAMA2015/blob/master/materials/labs/4_Thursday/Epigenetics_and_Chip_seq/Epigenetics_and_Chip_seqLab.pdf