1. spatialDE
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Update README

- More details
- Installation instructions
- Citation
- Add badges

Milan Malfait authored on 17/02/2021 11:04:01
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README.Rmd
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 # spatialDE
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 <!-- badges: start -->
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+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
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+[![R-CMD-check-bioc](https://github.com/sales-lab/spatialDE/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/sales-lab/spatialDE/actions)
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 <!-- badges: end -->
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-R wrapper for SpatialDE
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+The **spatialDE** package provides an R wrapper for the Python SpatialDE library,
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+using `r BiocStyle::CRANpkg("reticulate")` and `r BiocStyle::Biocpkg("basilisk")`.
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-[SpatialDE](https://github.com/Teichlab/SpatialDE) by [Svensson et al., 2018](https://www.nature.com/articles/nmeth.4636), is a method to identify spatially variable genes (SVGs) in spatially resolved
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-transcriptomics data.
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+[SpatialDE](https://github.com/Teichlab/SpatialDE), by [Svensson et al., 2018][Svensson2018],
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+is a method to identify spatially variable genes (SVGs) in spatially resolved transcriptomics data.
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+
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+This package started as part of the
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+[BiocSpatialChallenges](https://helenalc.github.io/BiocSpatialChallenges/index.html).
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+
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+
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+## Installation instructions
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+
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+<!-- Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `spatialDE` using from [Bioconductor](http://bioconductor.org/) the following code: -->
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+
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+<!-- ```{r 'install', eval = FALSE} -->
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+<!-- if (!requireNamespace("BiocManager", quietly = TRUE)) { -->
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+<!--     install.packages("BiocManager") -->
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+<!-- } -->
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+
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+<!-- BiocManager::install("spatialDE") -->
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+<!-- ``` -->
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+
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+The development version of **spatialDE** can be installed from
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+[GitHub](https://github.com/sales-lab/spatialDE) with:
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+
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+```{r 'install_dev', eval = FALSE}
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+if (!requireNamespace("BiocManager", quietly = TRUE)) {
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+    install.packages("BiocManager")
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+
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+BiocManager::install("sales-lab/spatialDE")
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+```
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+
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+## Citation
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+
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+Below is the citation output from using `citation('spatialDE')` in R. Please
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+run this yourself to check for any updates on how to cite __spatialDE__.
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+
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+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].
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+
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+```{r 'citation', eval = requireNamespace('spatialDE'), echo = FALSE, comment = ""}
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+print(citation('spatialDE'), bibtex = TRUE)
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+```
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+
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+
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+## Code of Conduct
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+
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+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.
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-## Aim of the repository
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-- create a wrapper for spatialDE in R, using `reticulate` and `basilisk`
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-- create a short script with an example workflow showing how to use the wrapper
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 ## Useful links
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-- [SpatialExperiment](https://github.com/drighelli/SpatialExperiment)
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+
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+- `r BiocStyle::Biocpkg("SpatialExperiment")`
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 - [BiocSpatialChallenges](https://helenalc.github.io/BiocSpatialChallenges/index.html)
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+
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+This package was developed using `r BiocStyle::Biocpkg('biocthis')`.
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+
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+[Svensson2018]: https://doi.org/10.1038/nmeth.4636
README.md
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@@ -5,23 +5,83 @@
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 <!-- badges: start -->
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+[![Lifecycle:
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+experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
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+[![R-CMD-check-bioc](https://github.com/sales-lab/spatialDE/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/sales-lab/spatialDE/actions)
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 <!-- badges: end -->
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-R wrapper for SpatialDE
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+The **spatialDE** package provides an R wrapper for the Python SpatialDE
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+library, using
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+*[reticulate](https://CRAN.R-project.org/package=reticulate)* and
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+*[basilisk](https://bioconductor.org/packages/3.12/basilisk)*.
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-[SpatialDE](https://github.com/Teichlab/SpatialDE) by [Svensson et
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-al., 2018](https://www.nature.com/articles/nmeth.4636), is a method to
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-identify spatially variable genes (SVGs) in spatially resolved
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-transcriptomics data.
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+[SpatialDE](https://github.com/Teichlab/SpatialDE), by [Svensson et al.,
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+2018](https://doi.org/10.1038/nmeth.4636), is a method to identify
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+spatially variable genes (SVGs) in spatially resolved transcriptomics
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+data.
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-## Aim of the repository
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+This package started as part of the
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+[BiocSpatialChallenges](https://helenalc.github.io/BiocSpatialChallenges/index.html).
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-  - create a wrapper for spatialDE in R, using `reticulate` and
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-    `basilisk`
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-  - create a short script with an example workflow showing how to use
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-    the wrapper
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+## Installation instructions
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+
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+<!-- Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `spatialDE` using from [Bioconductor](http://bioconductor.org/) the following code: -->
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+<!-- ```{r 'install', eval = FALSE} -->
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+<!-- if (!requireNamespace("BiocManager", quietly = TRUE)) { -->
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+<!--     install.packages("BiocManager") -->
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+<!-- } -->
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+<!-- BiocManager::install("spatialDE") -->
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+<!-- ``` -->
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+
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+The development version of **spatialDE** can be installed from
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+[GitHub](https://github.com/sales-lab/spatialDE) with:
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+
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+``` r
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+if (!requireNamespace("BiocManager", quietly = TRUE)) {
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+    install.packages("BiocManager")
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+
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+BiocManager::install("sales-lab/spatialDE")
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+```
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+
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+## Citation
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+
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+Below is the citation output from using `citation('spatialDE')` in R.
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+Please run this yourself to check for any updates on how to cite
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+**spatialDE**.
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+
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+Please note that this package merely provides a wrapper to use the
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+original Python methods in R. If you find these methods useful, please
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+also consider citing the [original
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+paper](https://doi.org/10.1038/nmeth.4636).
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+
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+
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+    To cite package 'spatialDE' in publications use:
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+
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+      Davide Corso and Milan Malfait (2021). spatialDE: R wrapper for
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+      SpatialDE. R package version 0.1.8.
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+      https://github.com/sales-lab/spatialDE
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+
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+    A BibTeX entry for LaTeX users is
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+
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+      @Manual{,
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+        title = {spatialDE: R wrapper for SpatialDE},
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+        author = {Davide Corso and Milan Malfait},
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+        year = {2021},
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+        note = {R package version 0.1.8},
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+        url = {https://github.com/sales-lab/spatialDE},
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+      }
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+
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+## Code of Conduct
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+
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+Please note that the **spatialDE** project is released with a
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+[Contributor Code of
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+Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
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+By contributing to this project, you agree to abide by its terms.
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 ## Useful links
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-  - [SpatialExperiment](https://github.com/drighelli/SpatialExperiment)
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-  - [BiocSpatialChallenges](https://helenalc.github.io/BiocSpatialChallenges/index.html)
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+-   *[SpatialExperiment](https://bioconductor.org/packages/3.12/SpatialExperiment)*
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+-   [BiocSpatialChallenges](https://helenalc.github.io/BiocSpatialChallenges/index.html)
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+
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+This package was developed using
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+*[biocthis](https://bioconductor.org/packages/3.12/biocthis)*.