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

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单细胞 RNA 表达数据在 Transformer 中的编码方法

逐段中英对照的技术综述：以 Geneformer、scGPT、scFoundation、scPRINT 与 UCE 为例，还原从 raw counts 到 token 与 embedding 的完整计算过程，比较信息保留、计算成本与适用场景，并给出可验证的实验设计。

从无生命到生命：物质、信息、自组织与涌现

一篇关于生命起源的深度综述：从亚里士多德与康德，到耗散结构、自催化闭合、RNA 复制、原始细胞与人工生命，梳理 2020–2026 年的实验与理论进展，并给出可检验的生命性评价框架。

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…