Repository for the single cell RNA sequencing data analysis for the human manuscript.

This is the GitHub repository for the single cell RNA sequencing data analysis for the human manuscript.

The following essential libraries are required for script execution:

• Seurat
• scReportoire
• ggplot2
• dplyr
• ggridges
• ggrepel
• ComplexHeatmap

Linked File:

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This repository contains code for the analysis of single cell RNA-seq dataset. The dataset contains raw FASTQ files, as well as, the aligned files that were deposited in GEO. Provided below are descriptions of the linked datasets:

1. Gene Expression Omnibus (GEO) ID: GSE229626 
   - Title: Gene expression profile at single cell level of human T cells stimulated via antibodies against the T Cell Receptor (TCR)
   - Description: This submission contains the `matrix.mtx`, `barcodes.tsv`, and `genes.tsv` files for each replicate and condition, corresponding to the aligned files for single cell sequencing data. 
   - Submission type: Private. In order to gain access to the repository, you must use a "reviewer token"(https://www.ncbi.nlm.nih.gov/geo/info/reviewer.html).

2. Sequence read archive (SRA) repository
    - Title: Gene expression profile at single cell level of human T cells stimulated via antibodies against the T Cell Receptor (TCR)
   - Description:  This submission contains the "raw sequencing" or `.fastq.gz` files, which are tab delimited text files. 
   - Submission type: Private. In order to gain access to the repository, you must use a "reviewer token" (https://www.ncbi.nlm.nih.gov/geo/info/reviewer.html). Please note that since the GSE submission is private, the raw data deposited at SRA may not be accessible until the embargo on GSE229626 has been lifted. 

 

Installation and Instructions
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The code included in this submission requires several essential packages, as listed above. Please follow these instructions for installation:

> Ensure you have R version 4.1.2 or higher for compatibility. 

> Although it is not essential, you can use R-Studios (Version 2022.12.0+353 (2022.12.0+353)) for accessing and executing the code. 

The following code can be used to set working directory in R:

> setwd(directory)

Steps:
1. Download the "Human_code_April2023.R" and "Install_Packages.R" R scripts, and the processed data from GSE229626.
2. Open "R-Studios"(https://www.rstudio.com/tags/rstudio-ide/) or a similar integrated development environment (IDE) for R. 
3. Set your working directory to where the following files are located:
   - Human_code_April2023.R
   - Install_Packages.R
4. Open the file titled `Install_Packages.R` and execute it in R IDE. This script will attempt to install all the necessary pacakges, and its dependencies.
 
5. Open the `Human_code_April2023.R` R script and execute commands as necessary.