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:
Footnotes
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Bioconda supports only Linux (64-bit and AArch64) and macOS (x86_64) ↩