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condense package list, remove R/RStudio instructions, refer to bioc-i… #55

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condense package list, remove R/RStudio instructions, refer to bioc-i…
andrewGhazi Oct 7, 2024
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Merge branch 'main' into upd_install
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145 changes: 8 additions & 137 deletions learners/setup.md
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Original file line number Diff line number Diff line change
Expand Up @@ -7,120 +7,9 @@ title: Setup
### R and RStudio

- R and RStudio are separate downloads and installations. R is a programming language and collection of software that implements that language. RStudio is a graphical integrated development environment
(IDE) that makes using R much easier and more interactive. You need to install R
(IDE) that makes using R easier and more interactive. You need to install R
before you install RStudio. After installing both programs, you will need to
install some R libraries from within RStudio. Follow the instructions below for
your operating system, and then follow the instructions to install packages.

### You are running Windows

<br>

::::::::::::::: solution

## If you already have R and RStudio installed

- Open RStudio, and click on "Help" > "Check for updates". If a new version is
available, quit RStudio, and download the latest version for RStudio.
- To check which version of R you are using, start RStudio and the first thing
that appears in the console indicates the version of R you are
running. Alternatively, you can type `sessionInfo()`, which will also display
which version of R you are running. Go on
the [CRAN website](https://cran.r-project.org/bin/windows/base/) and check
whether a more recent version is available. If so, please download and install
it. You can [check here](https://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-do-I-UNinstall-R_003f) for
more information on how to remove old versions from your system if you wish to do so.
- Follow the steps in the instructions [for everyone](#for-everyone) at the
bottom of this page.


:::::::::::::::::::::::::

::::::::::::::: solution

## If you don't have R and RStudio installed

- Download R from
the [CRAN website](https://cran.r-project.org/bin/windows/base/release.htm).
- Run the `.exe` file that was just downloaded
- Go to the [RStudio download page](https://www.rstudio.com/products/rstudio/download/#download)
- Under *All Installers* select **RStudio xxxx.yy.zz-uuu.exe - Windows 10/11** (where x, y, z, and u represent version numbers)
- Double click the file to install it
- Once it's installed, open RStudio to make sure it works and you don't get any
error messages
- Follow the steps in the instructions [for everyone](#for-everyone) at the
bottom of this page.

:::::::::::::::::::::::::

### You are running macOS

<br>

::::::::::::::: solution

## If you already have R and RStudio installed

- Open RStudio, and click on "Help" > "Check for updates". If a new version is
available, quit RStudio, and download the latest version for RStudio.
- To check the version of R you are using, start RStudio and the first thing
that appears on the terminal indicates the version of R you are running. Alternatively, you can type `sessionInfo()`, which will
also display which version of R you are running. Go on
the [CRAN website](https://cran.r-project.org/bin/macosx/) and check
whether a more recent version is available. If so, please download and install
it.
- Follow the steps in the instructions [for everyone](#for-everyone) at the
bottom of this page.


:::::::::::::::::::::::::

::::::::::::::: solution

## If you don't have R and RStudio installed

- Download R from
the [CRAN website](https://cran.r-project.org/bin/macosx/).
- Select the `.pkg` file for the latest R version
- Double click on the downloaded file to install R
- It is also a good idea to install [XQuartz](https://www.xquartz.org/) (needed
by some packages)
- Go to the [RStudio download page](https://www.rstudio.com/products/rstudio/download/#download)
- Under *All Installers* select **RStudio xxxx.yy.zz-uuu.dmg - macOS 10.15+** (where x, y, z, and u represent version numbers)
- Double click the file to install RStudio
- Once it's installed, open RStudio to make sure it works and you don't get any
error messages.
- Follow the steps in the instructions [for everyone](#for-everyone) at the
bottom of this page.


:::::::::::::::::::::::::

### You are running Linux

<br>

::::::::::::::: solution

## Install R using your package manager and RStudio

- Follow the instructions for your distribution
from [CRAN](https://cloud.r-project.org/bin/linux), they provide information
to get the most recent version of R for common distributions. For most
distributions, you could use your package manager (e.g., for Debian/Ubuntu run
`sudo apt-get install r-base`, and for Fedora `sudo yum install R`), but we
don't recommend this approach as the versions provided by this are
usually out of date. In any case, make sure you have at least R 4.2.0.
- Go to the [RStudio download
page](https://www.rstudio.com/products/rstudio/download/#download)
- Under *All Installers* select the version that matches your distribution, and
install it with your preferred method (e.g., with Debian/Ubuntu `sudo dpkg -i rstudio-xxxx.yy.zz-uuu-amd64.deb` at the terminal).
- Once it's installed, open RStudio to make sure it works and you don't get any
error messages.
- Follow the steps in the [instructions for everyone](#for-everyone)


:::::::::::::::::::::::::
install some R libraries from within RStudio. If you need to install R and/or RStudio, there are platform-specific installation instructions in the [Introduction to Bioconductor module](https://carpentries-incubator.github.io/bioc-intro/).

### For everyone

Expand All @@ -132,37 +21,19 @@ double-clicking the icon and enter these commands:
```r
install.packages(c("BiocManager", "remotes"))

BiocManager::install(c("AUCell", "batchelor", "BiocNeighbors",
"BiocParallel", "BiocSingular", "BiocStyle",
"bluster", "CuratedAtlasQueryR", "dplyr",
"DropletUtils", "edgeR", "EnsDb.Mmusculus.v79",
"ggplot2", "GSEABase", "MouseGastrulationData",
"pheatmap", "scater", "scDblFinder", "scran",
"scuttle", "Seurat", "SeuratData",
"SingleCellExperiment", "SingleR",
"TENxBrainData", "zellkonverter"),
BiocManager::install(c("AUCell", "batchelor", "BiocStyle",
"CuratedAtlasQueryR", "DropletUtils",
"EnsDb.Mmusculus.v79", "MouseGastrulationData",
"scDblFinder", "Seurat", "lgeistlinger/SeuratData",
"SingleR", "TENxBrainData", "zellkonverter"),
Ncpus = 4)
```

<!---
grep -Ph "library\(" episodes/*.Rmd | sort | uniq

^these are all libraries used in the episodes
^these are all libraries loaded in the episodes
-->

On the off chance your computer don't have multiple CPU cores, remove the `Ncpus
= 4` argument.

If you've worked with Bioconductor packages before, and the installation command
offers to update packages that have newer versions, saying something like:

```
<...long list of packages...>

Update all/some/none? [a/s/n]:
```

Select `n` for no. If old packages turn out to be a problem, cross that bridge
when you come to it.


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