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

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Proteomics by mass spectrometry: what is inside a raw file

A technical walkthrough of bottom-up proteomics: sample preparation, LC-MS/MS acquisition, the anatomy of vendor and open raw formats (mzML, mzMLb, imzML), reading data with…

Single-cell sequencing: from a cell to a cell state

A technical walkthrough of single-cell RNA-seq: molecular chemistry, platforms, raw file formats, barcode and UMI processing, count matrices, QC, clustering, annotation and…

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