I am trying to plot enriched functional clusters on each chromosome, like ideograms.
This is originally from the work that I was trying to find enriched functional clusters on chromosomes. I made 5-gene sliding 50-gene blocks and tested functional enrichment in each block.
The R package topGO can perform GO enrichment using Fisher's Exact test, which is based on gene counts, as well as Kolmogorov-Smirnov like test, which is based on gene scores.
The color attribute needs to be characters.
I have a bed file that containing all Isoseq reads and I would like to remove those overlapped with multiple genes in the annotation file.
I was trying to build genometools on my Mac laptop accoring to the INSTALL instructions but with no success.
Tried several tools to sort gff topologically, incluing genometools, Perl script GFF3sort, Python package tag and pure shell command.