---
title: "Downloading BUS data"
author: "Lambda Moses"
date: "`r Sys.Date()`"
output: BiocStyle::html_document
vignette: >
  %\VignetteIndexEntry{Downloading BUS data}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

This package provides the barcode, UMI, and set (BUS) format of the following datasets from 10X genomics:

* [100 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (v2 chemistry)](https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/hgmm_100)
* [1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (v3 chemistry)](https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/hgmm_1k_v3)
* [1k PBMCs from a Healthy Donor (v3 chemistry)](https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_1k_v3)
* [10k Brain Cells from an E18 Mouse (v3 chemistry)](https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/neuron_10k_v3)

The original fastq files have already been processed into the BUS format, which is a table with the following columns: barcode, UMI, equivalence class/set, and count (i.e. number of reads for the same barcode, UMI, and set). The datasets have been uploaded to `ExperimentHub`. This vignette demonstrates how to download the first dataset above with this package. See the [BUSpaRse website](https://bustools.github.io/BUS_notebooks_R/index.html) for more detailed vignettes.

```{r}
library(TENxBUSData)
library(ExperimentHub)
```

See which datasets are available with this package.
```{r}
eh <- ExperimentHub()
listResources(eh, "TENxBUSData")
```

In this vignette, we download the 100 cell dataset. The `force` argument will force redownload even if the files are already present.
```{r}
TENxBUSData(".", dataset = "hgmm100", force = TRUE)
```

Which files are downloaded?
```{r}
list.files("./out_hgmm100")
```

These should be sufficient to construct a sparse matrix with package [`BUSpaRse`](https://github.com/BUStools/BUSpaRse).