This is the repo I created for the bioinformatics project at SMTB. All the codes are just drafts, it is work in progress.
Results of of work can be found here.
- Pull this repo before you start some work and push it, when you have done something
- Attach meaningful messages to your commits, give your notebooks and other files clear names
- Branch, if you modified something, that other person also modified
- Before uploading the notebook, please, restart it and run all the cells to make sure, that all is ok
- Notebooks should be well formatted: structure it with headings in Markdown and briefly explain what is going on
- Imports and set up
- Get the data (read file into df, make API requests etc)
- Prepare the data (clean etc)
Do something meaningfulDo something else- Save the results (export some data if needed, save important figs etc)
In many notebooks there are some path constants, which should be changed to run the notebook, because you can store data in different places. Please, create such constants and add them to the beginning of your notebook into Imports ant set up section (like HTML_PATH)
We use conda to manage environments. To reproduce it, use env.yml file.
Data is NOT stored here, it is on our cluster. If you place some large datafiles in this folder locally, please, add it to .gitignore.
Here is the main folder on Google drive (access restricted): https://drive.google.com/drive/folders/1FeQQMyMXL3b7PiAs62wSqhbSsZpQOe76?usp=sharing
Different scripts and small text files with data related to data preprocessing