Single-cell Contamination Detection and Correction

https://github.com/zju-uoe-ccw-lab/sccdc
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single-cell Contamination Detection and Correction
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### Installing scCDC from GitHub in R

Source: https://github.com/zju-uoe-ccw-lab/sccdc/blob/main/README.md

This snippet demonstrates how to install the `scCDC` package directly from its GitHub repository in R. It first checks for the `devtools` package, installing it if necessary, and then uses `devtools::install_github` to install `scCDC`. This is a prerequisite for using the scCDC algorithm.

```R
if(!require("devtools", quietly = TRUE)){
  install.packages("devtools")
}

library(devtools)
install_github("ZJU-UoE-CCW-LAB/scCDC")
```

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### Installing Seurat V5 in R

Source: https://github.com/zju-uoe-ccw-lab/sccdc/blob/main/README.md

This code snippet shows how to install version 5 of the `Seurat` package in R. `Seurat` is a critical dependency for `scCDC`, as the current version of `scCDC` is built upon `Seurat` V5. This installation ensures compatibility and provides the necessary data structures for scCDC operations.

```R
install.packages('Seurat')
```

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### Accessing scCDC Package Vignettes in R

Source: https://github.com/zju-uoe-ccw-lab/sccdc/blob/main/README.md

This R command opens the vignettes (detailed documentation and tutorials) for the `scCDC` package. It provides comprehensive information on the `scCDC` method, its applications, and usage examples, serving as a primary resource for users seeking in-depth understanding.

```R
browseVignettes("scCDC")
```

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### Running scCDC Workflow on a Seurat Object in R

Source: https://github.com/zju-uoe-ccw-lab/sccdc/blob/main/README.md

This snippet outlines the typical workflow for applying `scCDC` to a Seurat object in R, assuming clustering information is present. It loads the `scCDC` library, reads a Seurat object, then sequentially performs contamination detection, quantification, and correction. The corrected data is set as the default assay for downstream analysis.

```R
library(scCDC)
seuratobject = readRDS('/path/to/seuratobject')
GCGs = ContaminationDetection(seuratobject)
contamination_ratio = ContaminationQuantification(seuratobject,rownames(GCGs))
seuratobj_corrected = ContaminationCorrection(seuratobject,rownames(GCGs))
DefaultAssay(seuratobj_corrected) = "Corrected"
```

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### Extracting Corrected Count Matrix from Seurat Object in R

Source: https://github.com/zju-uoe-ccw-lab/sccdc/blob/main/README.md

This R code snippet demonstrates how to extract the decontaminated count matrix from the `seuratobj_corrected` object generated by `scCDC`. It accesses the 'Corrected' assay's count layer and converts it into a data frame, making the decontaminated data available for further analysis.

```R
corrected_count_matrix = data.frame(seuratobj_corrected@assays[["Corrected"]]@layers$counts)
```
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