https://github.com/dmalzl/yorisc

A bit of code to interconvert objects between the Seurat and RISC environments for scRNA-seq data analysis
https://github.com/dmalzl/yorisc

bioinformatics scrna-seq-analysis seurat-objects

Last synced: 3 months ago
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A bit of code to interconvert objects between the Seurat and RISC environments for scRNA-seq data analysis

• Host: GitHub
• URL: https://github.com/dmalzl/yorisc
• Owner: dmalzl
• License: mit
• Created: 2021-07-06T15:27:57.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2021-07-08T14:18:04.000Z (almost 4 years ago)
• Last Synced: 2025-02-05T20:03:31.087Z (4 months ago)
• Topics: bioinformatics, scrna-seq-analysis, seurat-objects
• Language: R
• Homepage:
• Size: 13.7 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# yoRISC

A bit of code to interconvert objects between the Seurat and RISC environments for scRNA-seq data analysis.

This source was mainly compiled by following the [RISC guide](https://github.com/bioinfoDZ/RISC/blob/master/Seurat_to_RISC.pdf) to convert Seurat object to RISC object and getting insight from looking at the source code of the [Seurat package](https://github.com/satijalab/seurat) (mainly on how their IntegrateData and RunPCA methods would work). The code was tested with the main functionality of Seurat for a generic scRNA-seq analysis. To run the conversion functions as presented in the `conversion.R` script you need the following packages

- [RISC 1.0.0](https://github.com/bioinfoDZ/RISC)

- [SeuratDisk 0.0.0.9019](https://github.com/mojaveazure/seurat-disk)    

- [SeuratObject 4.0.0](https://github.com/mojaveazure/seurat-object)

- [Seurat 4.0.1](https://satijalab.org/seurat/articles/install.html)

For any additonal code presented in the `risc_integration.Rmd` you also have to install

- [gridExtra 2.3](https://cran.r-project.org/web/packages/gridExtra/index.html)

- [ggplot2 3.3.3](https://ggplot2.tidyverse.org/)

- [dplyr 1.0.5](https://dplyr.tidyverse.org/)

- [tidyverse 1.3.1](https://www.tidyverse.org/)

- [BiocManager 1.30.12](https://www.bioconductor.org/install/)

- [celldex 1.0.0](https://bioconductor.org/packages/release/data/experiment/html/celldex.html)

- [pheatmap 1.0.12](https://cran.r-project.org/web/packages/pheatmap/index.html)

- [SingleR 1.4.1](https://www.bioconductor.org/packages/release/bioc/html/SingleR.html)