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：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
