Create Monocle3.md

Author: epartan

scrnaseq/Monocle3.md

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+# Installation tips for Monocle3 on O2
+
+## You need to have certain modules loaded in your terminal or O2 Portal session
+
+1. Load required modules
+
+- `udunits` is required to install the `units` R package
+- `gdal`, `geos`, and, `proj` are required to install the `sf` R package
+
+Terminal:
+```
+ml gcc/14.2.0
+ml udunits/2.2.28 gdal/3.11.3 geos/3.13.1 proj/9.6.2 R/4.4.2
+```
+
+Package list to request O2 Portal RStudio session:
+```
+gcc/14.2.0 udunits/2.2.28 gdal/3.11.3 geos/3.13.1 proj/9.6.2 R/4.4.2
+```
+
+2. Start R
+
+3. Define your personal R package library
+
+We recommend making a separate library for each version of R.
+
+```
+userlib <- "~/R/4.4.2"
+```
+
+4. Install `units`
+
+```
+install.packages("units", lib = userlib, type = "source", repos = "https://cloud.r-project.org")
+```
+
+5. Install `sf`
+
+```
+install.packages("sf",    lib = userlib, type = "source", repos = "https://cloud.r-project.org")
+```
+
+6. Install `spdep`
+
+```
+install.packages("spdep", lib = userlib, type = "source", repos = "https://cloud.r-project.org")
+
+```
+
+7. Install the packages that [Monocle3](https://cole-trapnell-lab.github.io/monocle3/docs/installation/) actually tells you that it needs
+```
+remotes::install_github('satijalab/seurat-wrappers')
+BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats', 'limma',
+                       'lme4', 'S4Vectors', 'SingleCellExperiment', 'SummarizedExperiment',
+                       'batchelor', 'HDF5Array', 'ggrastr'),
+                     lib = userlib, lib.loc = userlib)
+remotes::install_github("bnprks/BPCells/r")
+remotes::install_github("cole-trapnell-lab/monocle3", lib = userlib, dependencies = FALSE)
+```