Multi -omics normalization examples and exercises

Multi -omics normalization exercises and examples for BIOINF 504
Two notebook files - one in python and one in R - are provided

For the the hands on exerience with tools that help with reproducibility (git, GitHub, documentstion )do a pull request against the following repo by the end of the class session:
https://github.com/mitreac/multi_omics_normalization

Make sure the pull request is done against the base (mitreac repo) not your forked repo main branch.
Here are the steps:

1. Fork the repo on GitHub:

https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo

On your local computer using a terminal (terminal, command prompt or git bash):

2. Clone the forked repo:

https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository

3. Create a new branch:

https://git-scm.com/book/en/v2/Git-Branching-Basic-Branching-and-Merging

4. Using you preferred coding IDE, do the exercises!

5. Extra exercise:

   • Add a function to complement a DNA sequence: A<->T, C<->G
   • Add an assert statement to test if the result of applying the function to the CGGAAT sequence matches the expected result GCCTTA
     On your local computer using a terminal (terminal, command prompt or git bash):

6. Check the status of your repo with:
   git status

7. Add and commit the change(s):

https://git-scm.com/docs/git-add

https://git-scm.com/docs/git-commit

Example:
git commit -m "Write commit message here"

8. Push the change to GitHub

https://git-scm.com/docs/git-push

You may be recommended to do:
git push --set-upstream origin your_branch

This is because your local branch (e.g: your_branch) does not have a corresponding branch in your forked repo on GitHub so you will tell the push command to create it.

9. Create a pull request agains the mitreac repo you forked.

After the push, in your forked repo on GitHub you will see a yellow banner that tells you to start a pull request.

The base repository should be the mitreac repo main branch and the head repo should be your forked repo the new branch (your_branch).

For the pull request: add a title, description, assignee, and label.

https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request-from-a-fork

10. Check that your pull request is in the list of the repo's pull requests:

https://github.com/mitreac/multi_omics_normalization/pulls