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spatialDE

R wrapper for SpatialDE

https://github.com/sales-lab/spatialde

Science Score: 49.0%

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
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 8 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.8%) to scientific vocabulary

Keywords

python r spatial-data transcriptomics wrapper

Keywords from Contributors

bioconductor gene bioconductor-package u24ca289073 immune-repertoire genomics sequencing ontology actions core-package
Last synced: 6 months ago · JSON representation

Repository

R wrapper for SpatialDE

Basic Info
  • Host: GitHub
  • Owner: sales-lab
  • License: other
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 1.47 MB
Statistics
  • Stars: 3
  • Watchers: 3
  • Forks: 3
  • Open Issues: 0
  • Releases: 0
Topics
python r spatial-data transcriptomics wrapper
Created about 5 years ago · Last pushed 10 months ago
Metadata Files
Readme License

README.Rmd 

---
output: github_document
---



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

# spatialDE


[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
[![R-CMD-check-bioc](https://github.com/sales-lab/spatialDE/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/sales-lab/spatialDE/actions)
[![Codecov test coverage](https://codecov.io/gh/sales-lab/spatialDE/branch/main/graph/badge.svg)](https://codecov.io/gh/sales-lab/spatialDE?branch=main)
[![BioC release status](http://www.bioconductor.org/shields/build/release/bioc/spatialDE.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/spatialDE)
[![BioC devel status](http://www.bioconductor.org/shields/build/devel/bioc/spatialDE.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/spatialDE)


The **spatialDE** package provides an R wrapper for the Python SpatialDE library,
using `r BiocStyle::CRANpkg("reticulate")` and `r BiocStyle::Biocpkg("basilisk")`.

[SpatialDE](https://github.com/Teichlab/SpatialDE), by [Svensson et al., 2018][Svensson2018],
is a method to identify spatially variable genes (SVGs) in spatially resolved transcriptomics data.

This package started as part of the
[BiocSpatialChallenges](https://helenalc.github.io/BiocSpatialChallenges/index.html).


## Installation instructions

Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then
install `r BiocStyle::Biocpkg("spatialDE")` from
[*Bioconductor*](http://bioconductor.org/) using the following code:

```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("spatialDE")
```

The development version of **spatialDE** can be installed from
[GitHub](https://github.com/sales-lab/spatialDE) with:

```{r 'install_dev', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
    
BiocManager::install("sales-lab/spatialDE")
```


## Basic usage

```{r usage, eval=TRUE}
library(spatialDE)
spe <- mockSVG(return_SPE = TRUE)
de_results <- spatialDE(spe)
head(de_results)
```


## Citation

Below is the citation output from using `citation('spatialDE')` in R. Please
run this yourself to check for any updates on how to cite __spatialDE__.

Please note that this package merely provides a wrapper to use the original Python methods in R. If you find these methods useful, please also consider citing the [original paper][Svensson2018].

```{r 'citation', eval = requireNamespace('spatialDE'), echo = FALSE, comment = ""}
print(citation('spatialDE'), bibtex = TRUE)
```


## Code of Conduct

Please note that the **spatialDE** project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.


## Useful links

- `r BiocStyle::Biocpkg("SpatialExperiment")`
- [BiocSpatialChallenges](https://helenalc.github.io/BiocSpatialChallenges/index.html)

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

[Svensson2018]: https://doi.org/10.1038/nmeth.4636

Owner

  • Name: Sales Lab
  • Login: sales-lab
  • Kind: organization

GitHub Events

Total
  • Push event: 3
Last Year
  • Push event: 3

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 235
  • Total Committers: 8
  • Avg Commits per committer: 29.375
  • Development Distribution Score (DDS): 0.545
Past Year
  • Commits: 17
  • Committers: 3
  • Avg Commits per committer: 5.667
  • Development Distribution Score (DDS): 0.471
Top Committers
Name Email Commits
davidecrs c****2@g****m 107
Milan Malfait m****4@g****m 106
Gabriele Sales g****s@g****m 11
Nitesh Turaga n****a@g****m 4
Lambda Moses d****2@c****u 3
J Wokaty j****y@s****u 2
Hervé Pagès h****b@g****m 1
Davide Corso 5****s 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1 caltech.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 8
  • Total pull requests: 18
  • Average time to close issues: 4 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 5
  • Total pull request authors: 4
  • Average comments per issue: 1.88
  • Average comments per pull request: 0.22
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
  • davidecrs (3)
  • milanmlft (2)
  • Vivianstats (1)
  • forrwill (1)
  • kinnaryshah (1)
Pull Request Authors
  • milanmlft (12)
  • davidecrs (4)
  • gbrsales (1)
  • lambdamoses (1)
Top Labels
Issue Labels
TODO (4) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 8,673 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: spatialDE

R wrapper for SpatialDE

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 8,673 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 5.1%
Stargazers count: 19.5%
Average: 21.5%
Downloads: 83.1%
Maintainers (1)
gabriele.sales@unipd.it
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.1 depends
  • Matrix * imports
  • S4Vectors * imports
  • SpatialExperiment * imports
  • SummarizedExperiment * imports
  • basilisk * imports
  • checkmate * imports
  • ggplot2 * imports
  • ggrepel * imports
  • gridExtra * imports
  • methods * imports
  • reticulate * imports
  • scales * imports
  • stats * imports
  • BiocStyle * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
.github/workflows/check-bioc.yml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite