单细胞轨迹分析

拟时间分析比较

http://genome.annoroad.com/News/Industry/1061.html

https://mp.weixin.qq.com/s?__biz=MzI1Njk4ODE0MQ==&mid=2247485775&idx=1&sn=5f258bed5b428b7cff2f70ce620decb0&chksm=ea1f0fcddd6886db8eb8e2b7b86c1bcc5009358b8e66bac9d5547e2a94337a24cf96c3153f52&scene=21#wechat_redirect

---

Velocity

在原有的UMAP上标注RNA velocity:https://cloud.tencent.com/developer/article/1620345

用Seurat做RNA Velocity: https://cloud.tencent.com/developer/article/1611587

Estimation on 10x data using loom and pagoda2: http://pklab.med.harvard.edu/velocyto/notebooks/R/DG1.nb.html

RNA速度-RNA velocity是什么: http://renyx.top/2019/11/01/RNA%E9%80%9F%E5%BA%A6-RNA-velocity%E6%98%AF%E4%BB%80%E4%B9%88/

Cell velocity: https://lazappi.github.io/phd-thesis-analysis/06-velocyto.html

Seurat2 with Veloctyo.R: https://github.com/velocyto-team/velocyto.R/issues/16

Estimating RNA Velocity using Seurat: https://github.com/satijalab/seurat-wrappers/blob/master/docs/velocity.md

velocyto简单使用: https://www.cnblogs.com/raisok/p/12425258.html

想分析单细胞RNA的动态变化？: https://wemp.app/posts/a33cc393-7255-4a7f-9f48-1b5bb15a118e

RNA velocity with kallisto | bus and velocyto.R: https://bustools.github.io/BUS_notebooks_R/velocity.html

RNA velocity | RNA速率: https://www.cnblogs.com/leezx/p/9504896.html

单细胞转录组数据分析|| scVelo 教程：RNA速率分析工具：https://www.jianshu.com/p/1e7acde1a318

---

Monocle2

        首先是自己使用monocle2的体会，一旦细胞数超过30k，monocel2便不能运行。但我查到一些帖子，有人也有用40k成功分析。如果有朋友遇到过类似的问题，可以一起探讨。

================================================================

Monocle2: https://github.com/cole-trapnell-lab/monocle2-rge-paper/blob/master/Supplementary_scripts/analysis_neuron_simulation_other_methods.r

Monocle2 & Diffusion map: https://nbisweden.github.io/excelerate-scRNAseq/session-trajectories/session-trajectories.html

Monocle2 踩坑教程: https://cloud.tencent.com/developer/article/1606510

使用monocle包进行pseudotime分析: https://www.jianshu.com/p/5d65c8a8671b

用Monocle进行伪时间分析: https://www.jianshu.com/p/aaa0c768c861

Monocle拟时间分析: https://www.jianshu.com/p/12ce02a032f9

使用monocle做单细胞谱系发育: https://zhuanlan.zhihu.com/p/111921087

monocle分析及结果解读: https://www.jianshu.com/p/e79ab1cc0a67

customer-defined colors：https://github.com/cole-trapnell-lab/monocle-release/issues/139

========================================================

Monocle3

monocle3 的安装: https://www.jianshu.com/p/79886c1affe5

scRNA-seq数据分析 || Monocle3: https://www.jianshu.com/p/e94cff521ebc

使用Monocle3对多样本单细胞数据进行伪时间分析: https://www.hongguangblog.cn/archives/monocle3

跟着官网学习单细胞Monocle3: https://www.jianshu.com/p/8f57ac63f399

拟时序分析后细胞类型按照不同state进行区分：http://www.bio-info-trainee.com/6293.html

单细胞测序第四期: 用Monocle进行伪时间分析：http://www.sci666.com.cn/1469.html

单细胞测序分析之Monocle2包学习笔记：https://www.jianshu.com/p/f6186755aae5

---

dyno

dyno使用教程--1个R包实现59种单细胞轨迹推断分析: https://cloud.tencent.com/developer/article/1606759

---

velocyto

Running velocyto on multiple samples with 10X：https://github.com/velocyto-team/velocyto.R/issues/54