RNA速率：数据读入

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://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/velocity.html

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

https://www.cnblogs.com/raisok/p/12425258.html

目录

RNA速率:软件下载与loom文件准备

RNA速率：数据读入

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。