生信R包安装

infercnv

需要先安装JAGS

JAGS手动安装失败

conda install jags 

进入R环境

install.packages("rjags")
if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
BiocManager::install("infercnv")
# test
library(infercnv)

Matrix

Seurat遇到以下bug，是因为Matrix在其他包安装过程中进行了更新，需要重新装回旧版本。

Error in validObject(.Object): invalid class “Graph” object: superclass "Mnumeric" not defined in the environment of the object's class

remove.packages("Matrix")
packageurl <- "https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/Archive/Matrix/Matrix_1.3-2.tar.gz"
install.packages(packageurl, repos=NULL, type="source")

Seurat

在R 3.6.3中安装

packageurl <- "https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_3.1.5.tar.gz"
install.packages(packageurl, repos=NULL, type="source")