1. monocle 2安装

方式一：官网安装方式

官网描述的是调用bioconductor.org中的biocLite.R脚本安装biocLite命令，但是按照下边命令总是报错，无法调用biocLite

source("http://bioconductor.org/biocLite.R") biocLite() biocLite("monocle")

于是在biocLite.R脚本中修改了一下，如下：

讯享网 Mirrors: uncomment the following and change to your favorite CRAN mirror if you don't want to use the default (cran.rstudio.com). options("repos" = c(CRAN="https://cran.rstudio.com")) Mirrors: uncomment the following and change to your favorite Bioconductor mirror, if you don't want to use the default (bioconductor.org) options("BioC_mirror" = "https://bioconductor.org") local({ vers <- getRversion() biocVers <- tryCatch({ BiocInstaller::biocVersion() # recent BiocInstaller }, error=function(...) { # no / older BiocInstaller BioC_version_associated_with_R_version <- get(".BioC_version_associated_with_R_version", envir=asNamespace("tools"), inherits=FALSE) if (is.function(BioC_version_associated_with_R_version)) BioC_version_associated_with_R_version() else # numeric_version BioC_version_associated_with_R_version }) if (vers > "2.13" && biocVers > "2.8") { if (exists("biocLite", .GlobalEnv, inherits=FALSE)) { txt <- strwrap("There is an outdated biocLite() function in the global environment; run 'rm(biocLite)' and try again.") stop("\n", paste(txt, collapse="\n")) } if (!suppressWarnings(require("BiocInstaller", quietly=TRUE))) { a <- NULL p <- file.path(Sys.getenv("HOME"), ".R", "repositories") if (file.exists(p)) { a <- tools:::.read_repositories(p) if (!"BioCsoft" %in% rownames(a)) a <- NULL } if (is.null(a)) { p <- file.path(R.home("etc"), "repositories") a <- tools:::.read_repositories(p) } if (!"package:utils" %in% search()) { path <- "//bioconductor.org/biocLite.R" txt <- sprintf("use 'source(\"https:%s\")' or 'source(\"http:%s\")' to update 'BiocInstaller' after library(\"utils\")", path, path) message(paste(strwrap(txt), collapse="\n ")) } else { if (vers >= "3.2.2" && vers < "3.3.0") { transitioning to https support; check availability con <- file(fl <- tempfile(), "w") sink(con, type="message") tryCatch({ xx <- close(file("https://bioconductor.org")) }, error=function(e) { message(conditionMessage(e)) }) sink(type="message") close(con) if (!length(readLines(fl))) a["BioCsoft", "URL"] <- sub("^http:", "https:", a["BioCsoft", "URL"]) } add a conditional for Bioc releases occuring WITHIN a single R minor version. This is so that a user with a version of R (whose etc/repositories file references the no-longer-latest URL) and without BiocInstaller will be pointed to the most recent repository suitable for their version of R if (vers >= "3.5.0") { a["BioCsoft", "URL"] <- sub(as.character(biocVers), "3.7", a["BioCsoft", "URL"]) } else if (vers >= "3.4.0") { a["BioCsoft", "URL"] <- sub(as.character(biocVers), "3.6", a["BioCsoft", "URL"]) } else if (vers >= "3.3.0") { a["BioCsoft", "URL"] <- sub(as.character(biocVers), "3.4", a["BioCsoft", "URL"]) } else if (vers >= "3.2") { a["BioCsoft", "URL"] <- sub(as.character(biocVers), "3.2", a["BioCsoft", "URL"]) } else if (vers == "3.1.1") { R-3.1.1's etc/repositories file at the time of the release of Bioc 3.0 pointed to the 2.14 repository, but we want new installations to access the 3.0 repository a["BioCsoft", "URL"] <- sub(as.character(biocVers), "3.0", a["BioCsoft", "URL"]) } else if (vers == "3.1.0") { R-devel points to 2.14 repository a["BioCsoft", "URL"] <- sub(as.character(biocVers), "2.14", a["BioCsoft", "URL"]) } else if (vers >= "2.15" && vers < "2.16") { a["BioCsoft", "URL"] <- sub(as.character(biocVers), "2.11", a["BioCsoft", "URL"]) biocVers <- numeric_version("2.11") } install.packages("BiocInstaller", repos=a["BioCsoft", "URL"]) if (!suppressWarnings(require("BiocInstaller", quietly=TRUE))) { path0 <- "//bioconductor.org/packages" path <- sprintf("%s/%s/bioc", path0, as.character(biocVers)) txt0 <- "'biocLite.R' failed to install 'BiocInstaller', use 'install.packages(\"BiocInstaller\", repos=\"https:%s\")' or 'install.packages(\"BiocInstaller\", repos=\"http:%s\")'" txt <- sprintf(txt0, path, path) message(paste(strwrap(txt), collapse="\n ")) } } } else { BiocInstaller version 1.16.0-1.18.1 do not automatically update when type=="source"; notify users when they have updated R over their old libraries installerVersion <- utils::packageVersion("BiocInstaller") test0 <- (vers > "3.1.2") && !identical(getOption("pkgType"), "source") && (installerVersion >= "1.16.0") && (installerVersion <= "1.16.4") if (test0) { if (installerVersion < "1.16.4") { txt <- "Update BiocInstaller with oldPkgType=options(pkgType=\"source\"); biocLite(\"BiocInstaller\"); options(oldPkgType)" message(paste(strwrap(txt, exdent=2), collapse="\n")) } if (vers >= "3.2") { path <- "//bioconductor.org/biocLite.R" txt <- sprintf("BiocInstaller version %s is too old for R version %s; remove.packages(\"BiocInstaller\"), re-start R, then source(\"https:%s\") or source(\"http:%s\")", biocVers, vers, path, path) warning(paste(strwrap(txt, exdent=2), collapse="\n")) } } } } else { tryCatch({ source("https://bioconductor.org/getBioC.R") }, error=function(e) { warning("https: failed (", conditionMessage(e), "), trying http", immediate.=TRUE) source("http://bioconductor.org/getBioC.R") }) biocLite <<- function(pkgs, groupName="lite", ...) { if (missing(pkgs)) biocinstall(groupName=groupName, ...) else biocinstall(pkgs=pkgs, groupName=groupName, ...) } } })

先在R中运行上边脚本，但前提是安装了最新的R（>2.13）和BiocInstaller（> 2.8）

讯享网

> BiocInstaller::biocVersion() [1] ‘3.7’ > getRversion() [1] ‘4.1.0’

方式二：Bioconductor安装方式（简单，直接，方便）

讯享网if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("monocle")

安装monocle依赖包

library(monocle) install.packages("devtools") devtools::install_github("cole-trapnell-lab/monocle-release@develop")

2. monocle3安装

先安装依赖包，可能会出现由于biocViews，RBGL（依赖包的依赖包）版本过低发生的报错，但并不是什么大问题，安装最新的版本即可

讯享网BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats', 'limma', 'S4Vectors', 'SingleCellExperiment', 'SummarizedExperiment', 'batchelor', 'Matrix.utils'))

安装monocle3

install.packages("devtools") devtools::install_github('cole-trapnell-lab/leidenbase') devtools::install_github('cole-trapnell-lab/monocle3') devtools::install_github('cole-trapnell-lab/monocle3', ref="develop") library(monocle3)