Recently I was trying to visualize the GWAS significant SNPs on chromosome to get a global view and to look for any clustering of significant SNPs in any region of chromosome. I found a software called Phenogram (see the attached link). I would like to know if anyone knows any software or R package similar to Phenogram.
http://visualization.ritchielab.psu.edu/phenograms/document
You may try Haploview. I used it to find Linkage disequilibrium between SNPs in the same gene, attached image showing distances between three SNPs and you can include many SNPs if you need and find if any two or more SNPs are inherited as one block
You could also take a look at ggbio. That has a variety of genomic visualisation tools that you can combine to create nice figures.
http://www.tengfei.name/ggbio/
@Peter Humberg, @Tao Zhou Circos and ggbio are awesome. Thanks a lot.
LocusZoom for a small region plot: http://csg.sph.umich.edu/locuszoom/
Haploview for genome-wide plot: http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview
- Badges
- Science topic
- Similar topics
- Mathematics
- Statistics
- Statistical Software
- R Statistical Package