Home

A working notebook of reproducible bioinformatics — genomes, structures, and data visualization.

Latest notes

From the notebook

Colorblind fridenly plotting in R

To use colorblind-friendly palettes in R, you mainly need the following packages. Be sure that we checked the plots with these packages before saving the plots. Thank you!

plotthis for R plotting

I noticed a new R package called “plotthis” produced byundefined. This package could generate publication ready plots with simple commands, which largely simplified the R…

ggtree for phylogenetic trees

Phylogenetic trees are used to show the evolutionary relationships between different species or genes. The ggtree package in R is a powerful tool for visualizing these…

tidyplots for R plotting

I noticed a new R package called “tidyplots” produced by Jan Broder Engler. This package could generate publication ready plots with simple commands, which largely…

Transfer GFF to GTF file

GFF3 (Generic Feature Format Version 3) file format represents the genomic features in a simple text-based tab-delimited file

gfatools for GFA (graphical fragment assembly) files

GFA (Graphical Fragment Assembly) format is used for sequence assembly graphs. It was proposed by Prof. Dr. Heng Li in 2014. Here is his proposal: https://lh3.github.io/2014…

Illustrate: Non-photorealistic Biomolecular Illustration

Illustrate is a small Fortran program for creating non-photorealistic illustrations of molecules, with cartoony colors and outlines, and soft ambient shadows. I originally…