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R_installations_spatial.md

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Spatial transcriptomics Nanocourse

Installation Requirements

Applications

Download the most recent versions of R and RStudio for your laptop:

Note 1: If you have a Mac with an M1 chip, download and install this tool before intalling your packages: https://mac.r-project.org/tools/gfortran-12.2-universal.pkg

Note 2: At any point (especially if you’ve used R/Bioconductor in the past), in the console R may ask you if you want to update any old packages by asking Update all/some/none? [a/s/n]:. If you see this, type "a" at the prompt and hit Enter to update any old packages. Updating packages can sometimes take quite a bit of time to run, so please account for that before you start with these installations.

Day 1 Module

(1) Install BiocManager:

if (!requireNamespace("BiocManager", quietly = TRUE)) 
    install.packages("BiocManager")

(2) Install SpatialFeatureExperiment v1.9.7+ :

ncpu = 2

BiocManager::install("pachterlab/SpatialFeatureExperiment",
                     ref = "devel",
                     Ncpus = ncpu)

(3) Install the remaining packages:

pkgs = c("SFEData",
         "scuttle",
         "scater",
         "scran",
         "bluster",
         "BiocParallel",
         "Voyager",
         "fastverse",
         "ggplot2",
         "pals")

BiocManager::install(pkgs,
                     Ncpus = ncpu)

Day 2 Module

(1) Install the packages listed below from CRAN using the install.packages() function.

  1. tidyverse
  2. Seurat
  3. patchwork
  4. qs
  5. quadprog
  6. remotes
  7. devtools

Please install them one-by-one as follows:

install.packages("tidyverse")
install.packages("Seurat")
install.packages("patchwork")
& so on ...

(2) Install the packages listed below from Bioconductor using the command below.

BiocManager::install("glmGamPoi")

(3) Install the packages listed below from GitHub using the given remotes:install_github or devtools::install_github command as provided below.

  1. SeuratWrappers: remotes::install_github('satijalab/seurat-wrappers')
  2. BANKSY: remotes::install_github("prabhakarlab/Banksy@devel")
  3. spacexr: devtools::install_github("dmcable/spacexr", build_vignettes = FALSE)

Loading libraries

Finally, please check that all the packages were installed successfully by loading them one at a time using the library() function.

## Day 1 module requirements
library(SpatialFeatureExperiment)
library(scuttle)
library(Voyager)
library(fastverse)
library(ggplot2)
library(SFEData)
library(scater)
library(scran)
library(bluster)
library(BiocParallel)
library(pals)


## Day 2 module requirements
library(qs)
library(Seurat)
library(tidyverse)
library(patchwork)
library(quadprog)
library(remotes)
library(devtools)
library(glmGamPoi)
library(SeuratWrappers)
library(Banksy)
library(spacexr)

Report successful installation

Once all packages have been loaded, run sessionInfo().

sessionInfo()