生物信息学

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记录一下论文中看到的单细胞分析R语言实现方法，主要是 Seurat、DESeq2、clusterProfiler (GO、KEGG)、GSEA。。。Seurat

pseudotime analysis / trajectory analysis：monocle，bioconductor/monocle

workflow：harmony-https://www.nature.com/articles/s41592-019-0619-0

gene marker ：COSG，https://academic.oup.com/bib/article/23/2/bbab579/6511197，https://github.com/genecell/COSG

T细胞亚群注释辅助工具：ProjecTILs ，Projecting scRNA-seq data onto a reference map，https://www.nature.com/articles/s41467-021-23324-4 ，https://carmonalab.github.io/ProjecTILs.demo/tutorial.html

upstream analysis : Cell Ranger 10XGenomics/cellranger https://www.nature.com/articles/ncomms14049

其他：

• UCSC Xena

• BD Bioscience

• Kaplan-Meier绘图仪

• ROC绘图仪

• Bioconda¹

Footnotes

1. Bioconda supports only Linux (64-bit and AArch64) and macOS (x86_64) ↩