There are many non-model organisms that do not have UTR annotations. Sometimes we may want to extract such regions to study regulatory activities.
I want to check if there are gene clusters (consecutive genes with the same function) on each chromosome. So I have the gene genomic orders (coordinates), and function (pfam/gene family etc) for each gene.
I wanted to test correlations between biological replicates of several samples in a ChIP-Seq experiment. Output better to be data frame with different features and samples.
I am trying to plot enriched functional clusters on each chromosome, like ideograms.
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.
Just a self-reminder.
If you are using a for loop to output multiple plots, ggplot doesn't work.