参考链接:
https://github.com/velocyto-team/velocyto.R
http://velocyto.org/velocyto.py/index.html
http://pklab.med.harvard.edu/velocyto/notebooks/R/chromaffin2.nb.html
https://github.com/velocyto-team/velocyto.R/issues/16
https://www.cnblogs.com/raisok/p/12425258.html
目录
RNA速率：使用Seurat的结果做RNA velocity
velocyto.R的安装
loom文件生成后，接下来将使用velocyto.R对loom文件进行分析
library(devtools)
install_github("velocyto-team/velocyto.R")
数据读入
>library(velocyto.R)
>setwd("/datadisk02/Jiawei_Wang_2019")
>wt<-read.loom.matrices("WANG/velocyto/WANG.loom")
reading loom file via hdf5r...
>str(wt1)
List of 3
$ spliced :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
$ unspliced:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
$ ambiguous:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
>save(wt,file="WT-loom.rds")
>emat<-WT$spliced
#做直方图查看数据分步
>hist(log10(colSums(emat)),col='wheat',xlab='cell size')
后续过程我想用Seurat的聚类进行分析，所以velocyto.R的聚类就不运行了。
