Question: Newbie - Plotting Genes on Genomic Axis and Creating a Genomic Browser
0
gravatar for berrysweetpie
3.9 years ago by
United States
berrysweetpie0 wrote:

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?

sequencing gen • 1.5k views
ADD COMMENTlink modified 3.9 years ago by Asaf5.6k • written 3.9 years ago by berrysweetpie0

If I may, reinventing the wheel is a waste of time - unless you are doing it as a personnal 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 functionnalities to implement.

ADD REPLYlink written 3.9 years ago by cyril-cros890

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

ADD REPLYlink written 3.9 years ago by berrysweetpie0
2

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.

ADD REPLYlink written 3.9 years ago by dandan350

Awesome, thanks for all your help!

ADD REPLYlink written 3.9 years ago by berrysweetpie0

(sorry duplicate post)

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by dandan350
2
gravatar for Asaf
3.9 years ago by
Asaf5.6k
Israel
Asaf5.6k wrote:

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

ADD COMMENTlink written 3.9 years ago by Asaf5.6k
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