generate_workshop_data.qmd

---
title: "Create Demo Data for SCRGOT Workshop"
author: "Matt Cannon and Corinne Strawser"
date: "`r format(Sys.time(), '%m/%d/%Y')`"
format:
    html:
        toc: true
        toc_float: true
        toc_depth: 5
        number_sections: false
        code-fold: true
        code-link: true
        df-print: kable
        embed-resources: true
        self_contained: true
execute:
    cache: true
knitr:
    opts_chunk:
        cache.lazy: false
        warning: false
        message: false
lightbox: true
---

```{r setup}
#| include: FALSE
library(rrrSingleCellUtils)
library(Seurat)
# library(DropletUtils)
library(qs)
library(tidyverse)
theme_set(theme_bw())
theme_update(plot.title = element_text(hjust = 0.5))
library(patchwork)

set.seed(1337)
```

# Set up directory structure
```{bash mkdirs}
for directoryName in \
    output \
    output/rdata \
    output/rdata_premade \
    output/figures \
    input/multiomics \
    input/scRNA \
    input/spatial
do
    if [ ! -d ${directoryName} ]
    then
        mkdir -p ${directoryName}
    fi
done
```

# Process in snRNA-seq from aging mouse brain

{{< include workshop_data/allen_brain_mouse_aging_snrna.rmd >}}

# Get brain reference data for cell type annotation

{{< include workshop_data/brain_ref_data.qmd >}}

# Make all pre-made Seurat objects

{{< include workshop_data/make_scrna_objects.qmd >}}

# Make pre-made Seurat objects for spatial data

{{< include workshop_data/make_visium_objects.rmd >}}

# Download multiome data
```{bash download_multiome}
source workshop_data/download_multiome.sh
```

# Download model data for nichenetr
```{bash download_nichenetr}
source workshop_data/download_nichenetr.sh
```

# Session information
```{r session_info}
#| include: FALSE
sessionInfo()
```