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SpotSweeper

Spatially-aware quality control for spatial transcriptomics

https://github.com/mictott/spotsweeper

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.1%) to scientific vocabulary

Keywords

bioconductor quality-control spatial-transcriptomics
Last synced: 6 months ago · JSON representation

Repository

Spatially-aware quality control for spatial transcriptomics

Basic Info
Statistics
  • Stars: 12
  • Watchers: 4
  • Forks: 1
  • Open Issues: 6
  • Releases: 0
Topics
bioconductor quality-control spatial-transcriptomics
Created over 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct Support

README.Rmd 

---
output: github_document
---



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

# SpotSweeper 


[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![codecov](https://codecov.io/gh/MicTott/SpotSweeper/graph/badge.svg?token=M1MUJN7VS6)](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')`.

Owner

  • Name: Michael Totty
  • Login: MicTott
  • Kind: user

GitHub Events

Total
  • Issues event: 11
  • Watch event: 6
  • Issue comment event: 11
  • Push event: 19
  • Fork event: 1
Last Year
  • Issues event: 11
  • Watch event: 6
  • Issue comment event: 11
  • Push event: 19
  • Fork event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 22
  • Total pull requests: 2
  • Average time to close issues: 3 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 8
  • Total pull request authors: 2
  • Average comments per issue: 1.27
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 0
  • Average time to close issues: 3 days
  • Average time to close pull requests: N/A
  • Issue authors: 5
  • Pull request authors: 0
  • Average comments per issue: 2.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • MicTott (8)
  • boyiguo1 (7)
  • estellad (1)
  • jac-thom (1)
  • lambdamoses (1)
  • gitMakeCoffee (1)
  • ashishjain1988 (1)
  • ppm1337 (1)
Pull Request Authors
  • MicTott (2)
  • boyiguo1 (2)
Top Labels
Issue Labels
documentation (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 4,170 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
bioconductor.org: SpotSweeper

Spatially-aware quality control for spatial transcriptomics

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 4,170 Total
Rankings
Dependent repos count: 0.0%
Average: 15.6%
Dependent packages count: 31.3%
Maintainers (1)
mictott@gmail.com
Last synced: 6 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.5.0 composite
  • actions/checkout v4 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 4.3 depends
  • BiocNeighbors * imports
  • BiocParallel * imports
  • MASS * imports
  • SingleCellExperiment * imports
  • SpatialExperiment * imports
  • SummarizedExperiment * imports
  • dbscan * imports
  • stats * imports
  • STexampleData * suggests
  • escheR * suggests
  • ggpubr * suggests
  • knitr * suggests
  • scuttle * suggests
  • testthat * suggests