README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)
```

# SpotSweeper <img src="man/figures/hexsticker.png" align="right" style="width:200px;" />

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`SpotSweeper` is a package developed for spatially-aware quality control (QC) methods for the detection, visualization, and removal of both local outliers and regional artifacts in spot-based spatial transcriptomics data, such as 10x Genomics `Visium`, using standard QC metrics. 

If you experience any issues using the package or would like to make a suggestuin, please open an issue on the [GitHub repository](https://github.com/MicTott/SpotSweeper/issues).

To find more information, please visit the [documentation website](http://MicTott.github.io/SpotSweeper).

```{r schematic, echo=FALSE, out.width = '100%'}
knitr::include_graphics("./man/figures/schematic.png")
```


## Installation instructions

You can install the latest version of `SpotSweeper` from Bioconductor with the following code: 
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("SpotSweeper")
```

The latest development version can be installed from [GitHub](https://github.com/MicTott/SpotSweeper) using the following: 

```{r 'install_dev', eval = FALSE}
if (!require("devtools")) install.packages("devtools")
remotes::install_github("MicTott/SpotSweeper")
```

## Tutorials

A detailed tutorial is available in the package vignette from Bioconductor. A direct link to the tutorial / package vignette is available [here](https://mictott.github.io/SpotSweeper/articles/getting_started.html).


## Development tools

- Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)  through `BiocStyle::Biocpkg('biocthis')`.
-  The [documentation website](http://MicTott.github.io/SpotSweeper) is automatically updated thanks to `BiocStyle::CRANpkg('pkgdown')`.
-  The code is styled automatically thanks to `BiocStyle::CRANpkg('styler')`.
-  The documentation is formatted thanks to `BiocStyle::CRANpkg('devtools')` and `BiocStyle::CRANpkg('roxygen2')`.

This package was developed using `BiocStyle::Biocpkg('biocthis')`.