tools for calculating nucleotide composition of a gene

Question

[xiaoleiusc]

Hi, All,

I wonder if there is any tool to do nucleotide composition analysis to generate figures such as this (link here)? It would be great if the sliding window size could be customized.

Thanks,

Xiao

[cpad0112]

Visualize nucleotides for every position in R

Answer 1

[bernatgel]

You should be able to compute the actual nucleotide composition with Biostrings and compute the rolling mean with zoo::rollmean. To plot these values you can use karyoploteR. This example at the karyoploteR tutorial does not do a rolling mean but computed the mean over fixed tiling, but it can help you get started.