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https://github.com/robaina/dokdonia
Source code employed in the study: Gene expression response to temperature acclimation in a model photoheterotrophic marine flavobacterium
https://github.com/robaina/dokdonia
differential-expression dokdonia temperature transcription
Last synced: 2 days ago
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Source code employed in the study: Gene expression response to temperature acclimation in a model photoheterotrophic marine flavobacterium
- Host: GitHub
- URL: https://github.com/robaina/dokdonia
- Owner: Robaina
- Created: 2021-03-05T13:45:32.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-06-19T08:08:21.000Z (5 months ago)
- Last Synced: 2024-10-17T19:38:46.244Z (20 days ago)
- Topics: differential-expression, dokdonia, temperature, transcription
- Language: Python
- Homepage:
- Size: 239 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# :bulb: About
This repo contains the source code employed in the study "Gene expression response to temperature acclimation in a model photoheterotrophic marine flavobacterium". Source code is organized into a Python package, and dependencies are managed with Conda.
## :wrench: Installation
To install the package, clone the repo and run the setup script:
```bash
git clone https://github.com/Robaina/Dokdonia.git
cd Dokdonia
bash setup.sh
```
## :rocket: Usage
To use the package, activate the Conda environment:
```bash
conda activate dokdonia
```
This environment includes a Jupyter Notebook ipykernel, so the package can be used in a notebook as well.
## :notebook_with_decorative_cover: Notebooks
The steps followed to generate the results and figures in the paper are detailed in the following notebooks:
- [Differential expression](notebooks/1_differential_expression.ipynb)
- [Clustering: DeSeq2-normalized counts](notebooks/2_clustering_deseq2.ipynb)
- [Clustering: Transcript abundances](notebooks/3_clustering_tc.ipynb)
- [Figures](notebooks/4_paper_figures.ipynb)