https://github.com/mictott/spotsweeper
Spatially-aware quality control for spatial transcriptomics
https://github.com/mictott/spotsweeper
bioconductor quality-control spatial-transcriptomics
Last synced: 4 months ago
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Spatially-aware quality control for spatial transcriptomics
- Host: GitHub
- URL: https://github.com/mictott/spotsweeper
- Owner: MicTott
- License: mit
- Created: 2023-10-30T20:12:02.000Z (over 1 year ago)
- Default Branch: devel
- Last Pushed: 2024-12-24T15:16:25.000Z (5 months ago)
- Last Synced: 2025-01-20T06:43:40.316Z (4 months ago)
- Topics: bioconductor, quality-control, spatial-transcriptomics
- Language: R
- Homepage: https://mictott.github.io/SpotSweeper/
- Size: 36.9 MB
- Stars: 5
- Watchers: 3
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Support: .github/SUPPORT.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# SpotSweeper 
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://codecov.io/gh/MicTott/SpotSweeper)
`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')`.