R packages

了解如何创建包的网站：http://r-pkgs.had.co.nz/

1、What are repositories（仓库）?

A repository is a central location where many developed packages are located and available for download.

There are three big repositories:

1. CRAN (Comprehensive R Archive Network): R’s main repository (>12,100 packages available!)

2. BioConductor: A repository mainly for bioinformatic-focused packages

3. GitHub: A very popular, open source repository (not R specific!)

2、怎样找到所需要的包

（1）CRAN 将所有包分成35个主题，可以根据自己感兴趣的进行查看

https://cran.r-project.org/web/views/

（2）R包的一个搜索引擎，可以找到来自 CRAN, BioConductor, and GitHub的包

https://www.rdocumentation.org/

1. 下载包

Installing packages from CRAN through R/RStudio

1、代码

install.packages("ggplot2")
install.packages(c("ggplot2","devtools","lme4""))

1. 框框（不知道怎么描述）

Installing from Bioconductor（https://www.bioconductor.org/install/）

首先下载BiocManager,若已经下载就可以跳过这步

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.16")

下载bioconductor中的包

BiocManager::install(c("GenomicFeatures", "AnnotationDbi"))

Installing from GitHub（https://kbroman.org/pkg_primer/pages/github.html）

首先下载devtools package.

install.packages("devtools")

然后加载

library(devtools)

最后载入github上的包

install_github("author/package")

例子https://github.com/kbroman/broman

install_github("kbroman/broman")