DGE_Candida_albicans

code for differential gene expression of Candida albicans

Differential Gene Expression Analysis for Candida albicans

This repository contains the code, data, and results for the differential gene expression (DGE) analysis of Candida albicans.

Files and Directories

• dge_analysis.R: R script for running the DGE analysis.
• data/: Input files for the analysis.
  • data_for_dge_csv.csv: Raw count data.
  • DGE_FILE_DATA.txt: Metadata file.
• results/: Output files generated from the analysis.
  • cts_integer.csv: Normalized count data.
  • top_diff_expressed_genes.csv: Top differentially expressed genes.
• visualizations/: Visual plots generated during the analysis.

Prerequisites

• R (version X.X.X or higher)
• Required R libraries: DESeq2, ggplot2, pheatmap, writexl, reshape2, plotly

Running the Analysis

1. Clone the repository:

   git clone https://github.com/your-username/DGE_Candida_Albicans.git
   cd DGE_Candida_Albicans

2. Install required R packages:

   install.packages(c("DESeq2", "ggplot2", "pheatmap", "writexl", "reshape2", "plotly"))

3. Run the R script:

   source("dge_analysis.R")

Contact

For questions or feedback, contact Dhruva Tirumalasetty at [email protected] .