Functional genomic analysis of genes important for Candida albicans fitness in diverse environmental conditions

Overview

This repository contains data, Jupyter notebooks, and source code for conducting a functional genomic analysis of genes important for Candida albicans fitness in diverse environmental conditions. The analysis was performed using Python and R.

Project Structure

The repository is organized as follows:

• data/: Contains the datasets and relevant data files used in the analysis.
• notebooks/: Jupyter notebooks for step-by-step data analysis, visualization, and interpretation.
• src/: Source code for Python and R scripts used in the analysis.
• STAR_Protocols_code_data/: Example code and data for running through the scoring pipeline from raw reads.

Prerequisites & Installation

To run the analysis and reproduce the results, you'll need the following software and packages installed:

Python

• Python 3.9
• numpy (1.20.3)
• pandas (1.3.4)
• matplotlib (3.4.3)
• seaborn (0.11.2)
• scipy (1.10.1)

R

• limma
• pheatmap
• RColorBrewer
• plotrix
• FLEX (https://github.com/csbio/FLEX_R)
• ggplot2
• ggthemes
• gplots
• ggrepel
• reshape2
• GGally
• dplyr
• tidyr
• ggvenn

Sequence alignment

• See src/barseq_to_reads/barseq_assignreads.txt for details

License

Distributed under the MIT License. See LICENSE for more information.

Contact

Please email to Xiang Zhang (zhan6668@umn.edu) if you have any questions, comments, or suggestions regarding this program.

Project Link: https://github.com/csbio/C.albicans_in_vitro_pipeline

Publication: Xiong, E. H., Zhang, X., Yan, H., Ward, H. N., Lin, Z. Y., Wong, C. J., Fu, C., Gingras, A. C., Noble, S. M., Robbins, N., Myers, C. L. & Cowen, L. E. (2024). Functional genomic analysis of genes important for Candida albicans fitness in diverse environmental conditions. Cell Reports, 43(8). (DOI: 10.1016/j.celrep.2024.114601)