很久沒(méi)有做擬時(shí)了，之前在官網(wǎng)上看到這樣一個(gè)消息，我想還是需要解讀和演示下monocle3。
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http://cole-trapnell-lab.github.io/monocle-release/docs/
Monocle原理算法文章參考：
http://cole-trapnell-lab.github.io/monocle-release/papers/monocle2、monocle3 alpha廢棄并不代表不能用了，結(jié)果不好了，只是Monocle3更新了功能，優(yōu)化了分析而已，而且分析操作更簡(jiǎn)單、簡(jiǎn)潔（個(gè)人感覺(jué)）。話不多說(shuō)，還是直接進(jìn)入Monocle3，看看怎么進(jìn)行單細(xì)胞擬時(shí)分析吧！
https://cole-trapnell-lab.github.io/monocle3/Monocle3主要可執(zhí)行三種分析功能:
Clustering, classifying, and counting cells. Single-cell RNA-Seq experiments allow you to discover new (and possibly rare) subtypes of cells. Monocle 3 helps you identify them.
Constructing single-cell trajectories. In development, disease, and throughout life, cells transition from one state to another. Monocle 3 helps you discover these transitions.
Differential expression analysis. Characterizing new cell types and states begins with comparisons to other, better understood cells. Monocle 3 includes a sophisticated, but easy-to-use system for differential expression.
Monocle 3是基于R環(huán)境分析的，R版本需4.1.0或更高、Bioconductor版本3.14及以上和monocle3 1.2.7或更高版本才能訪問(wèn)最新功能?？傊?，重新安裝下Monocle3，其他依賴包也更新下！注意：我安裝的時(shí)候出現(xiàn)了問(wèn)題，Matrix.utils包不適用于monocle3，按照BiocManager去安裝更新，結(jié)果一眾大包都不能正常加載了，后來(lái)更新了Rtools，總算正常了，可是monocle3依然不行。最后選擇直接下載Matrix.utils壓縮包安裝，就成功了。
擬時(shí)推斷：
可視化1：module
可視化2：gene expression
可視化3：分組
