Skip to content

Latest commit

 

History

History
63 lines (41 loc) · 1.98 KB

README.md

File metadata and controls

63 lines (41 loc) · 1.98 KB
Raw

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

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 ([email protected]) 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)