之前cellranger count以及aggr拿到了三组表达矩阵文件,后续使用seurat等R包进行处理
配置:
Linux/R4.1.0
1.安装BiocManager
> install.packages("BiocManager")
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors
.
21: China (Guangzhou) [https]
.
Selection: 21
* DONE (BiocManager)
The downloaded source packages are in
‘/tmp/Rtmpn99W31/downloaded_packages’
# 安装成功
> library(BiocManager)
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
2. 安装Seurat等
第一次装,问题真多,小白头疼
> BiocManager::install("Seurat")
.
.
# 疯狂error,查看
> warnings()
Warning messages:
1: In .inet_warning(msg) :
installation of package ‘caTools’ had non-zero exit status
2: In .inet_warning(msg) :
installation of package ‘sitmo’ had non-zero exit status
3: In .inet_warning(msg) :
installation of package ‘openssl’ had non-zero exit status
4: In .inet_warning(msg) :
installation of package ‘htmlwidgets’ had non-zero exit status
5: In .inet_warning(msg) :
installation of package ‘crosstalk’ had non-zero exit status
6: In .inet_warning(msg) :
installation of package ‘RSpectra’ had non-zero exit status
7: In .inet_warning(msg) :
installation of package ‘future’ had non-zero exit status
8: In .inet_warning(msg) :
installation of package ‘miniUI’ had non-zero exit status
9: In .inet_warning(msg) :
installation of package ‘patchwork’ had non-zero exit status
10: In .inet_warning(msg) :
installation of package ‘RcppAnnoy’ had non-zero exit status
11: In .inet_warning(msg) :
installation of package ‘reticulate’ had non-zero exit status
12: In .inet_warning(msg) :
installation of package ‘Rtsne’ had non-zero exit status
13: In .inet_wa