# R package installation references

This section collects MSI Help Desk reference notes for R packages that have needed package-specific installation steps.

## General guidance

- Run package installs in an interactive compute session when possible.
- Match `options(Ncpus = ...)` to the number of tasks allocated to your session to speed up package builds.
- Load any required system modules both when installing the package and when using it later.
- For packages that take several minutes to compile, a Persistent Desktop session can also work well.

Example interactive session:

```bash
srun -N 1 -n 10 --mem 10G -t 20 -p msismall --pty bash
```

Example R session setup:

```r
R
options(Ncpus = 10)
```

## Package references

- [azimuth](./azimuth.md)
- [bnlearn](./bnlearn.md)
- [brms](./brms.md)
- [CellChat](./cellchat.md)
- [clusterProfiler](./clusterprofiler.md)
- [circular](./circular.md)
- [devtools](./devtools.md)
- [effsize](./effsize.md)
- [emmeans](./emmeans.md)
- [ggeffects](./ggeffects.md)
- [ggpattern](./ggpattern.md)
- [ggplot2](./ggplot2.md)
- [lme4](./lme4.md)
- [lmerTest](./lmertest.md)
- [loo](./loo.md)
- [ragg](./ragg.md)
- [readxl](./readxl.md)
- [rstan](./rstan.md)
- [sf](./sf.md)
- [terra](./terra.md)
- [tidyverse](./tidyverse.md)
- [writexl](./writexl.md)

```{toctree}
:maxdepth: 1
:hidden:

azimuth
bnlearn
brms
cellchat
clusterprofiler
circular
devtools
effsize
emmeans
ggeffects
ggpattern
ggplot2
lme4
lmertest
loo
ragg
readxl
rstan
sf
terra
tidyverse
writexl
```