Single Cell Quality Control and Integration Pipeline with Seurat

This repository contains an R script for a pipeline designed to automate single-cell quality control and sample integration in Seurat using the output from Cell Ranger. The pipeline utilizes various R packages including dplyr, Seurat, ggplot2, sctransform, glmGamPoi, and tidyverse.

Usage:

1. Clone the Repository:

    git clone https://github.com/your_username/Single-Cell-QC-Integration-Pipeline.git

2. Place Cell Ranger Output Files: Place your Cell Ranger output folders in the same folder as the R script.

3. Run the Pipeline: Open your terminal or command prompt, navigate to the folder containing the R script and Cell Ranger output files, and execute the following command:

    Rscript single_cell_pipeline.R

Output:

Upon successful execution, the pipeline will generate:

• A folder containing quality control plots.
• A Seurat object with integrated samples.

Requirements:

R (version >= 3.5.0) Required R Packages:

• dplyr
• Seurat
• ggplot2
• sctransform
• glmGamPoi
• tidyverse

Notes:

Ensure that all required R packages are installed in your R environment prior to running the pipeline. Make sure that your Cell Ranger output files are appropriately formatted and contain necessary information for the pipeline to execute successfully.