initial commit

[danhtruong]

Hi there, thanks for your contribution!
Please fill out this template to help us review your code.

Remember, the more context you provide, the faster the review will go!
For more information about filling out this template, please see the OpenScPCA documentation on filing pull requests:
https://openscpca.readthedocs.io/en/latest/contributing-to-analyses/creating-pull-requests/

Before filing the pull request, you can also feel free to delete the italicized instruction lines in this template.

Purpose/implementation Section

In this section, tell reviewers about the scope and purpose of the code in the pull request.

Please link to the GitHub issue that this pull request addresses.

#701
If applicable, you can also link to the associated GitHub Discussion.
#583

What is the goal of this pull request?

Initiate the script
Analyze DSRCT-specific genes in the samples
Identify tumor and normal cells

Briefly describe the general approach you took to achieve this goal.

Assessed gene expression in the cells
Used a z-score to determine tumor vs normal where z-score >0 is a tumor cell
It did not work well and we will try alternative methods

If known, do you anticipate filing additional pull requests to complete this analysis module?

Yes. I will add additional pull requests to use SingleR or similar method and signature based method like AUC.

Results

Delete this section if no results are associated with your pull request.

In this section, tell reviewers about what kinds of results (if any) your code produces.

What is the name of your results bucket on S3?

Results should be uploaded to your bucket so they are available during review.
See here for instructions on how to upload to your bucket:
https://openscpca.readthedocs.io/en/latest/software-platforms/aws/working-with-s3-buckets/

What types of results does your code produce (e.g., table, figure)?

What is your summary of the results?

Provide directions for reviewers

Initial commit

What are the software and computational requirements needed to be able to run the code in this PR?

Nothing but local machine and R.

Are there particularly areas you'd like reviewers to have a close look at?

Is there anything that you want to discuss further?

Author checklists

Check all those that apply.
Note that you may find it easier to check off these items after the pull request is actually filed.

Analysis module and review

• [x ] This analysis module uses the analysis template and has the expected directory structure.
• [x ] The analysis module README.md has been updated to reflect code changes in this pull request.
• [x ] The analytical code is documented and contains comments.
• [ x] Any results and/or plots this code produces have been added to your S3 bucket for review.

Reproducibility checklist

• Code in this pull request has been added to the GitHub Action workflow that runs this module.
• The dependencies required to run the code in this pull request have been added to the analysis module Dockerfile.
• If applicable, the dependencies required to run the code in this pull request have been added to the analysis module conda environment.yml file.
• If applicable, R package dependencies required to run the code in this pull request have been added to the analysis module renv.lock file.

[jashapiro]

Hello Danh, thank you for your first contribution! It was great to meet you at the AACR peds meeting, and I look forward to working with you on this and also helping out with anything you might need running scpca-nf for your contribution to the portal.

I know you filed this as a draft, but as this is a Friday, I thought I would jump in with some quick comments before you get too far down the path.

It looks like you did run our setup script, which is great. For this first PR, you might want to include only those files, so we can have a smaller PR with just the analysis notebook that you added in a later PR.

So for this first PR, you might want to just update the README with a bit more about your planned analysis (it does not need to be complete at this stage), and temporarily remove your analysis notebooks, and then we should be able to get this first PR in pretty quickly.

Finally, I recommend using branches in your fork to help keep each PR separate, rather than making all of your changes in main. Let me know if you have any questions about that: I don't want to make any assumptions about your level of expertise with git and the kinds of PR processes that we are using in this project!

Finally, if you are a Slack user, I wanted to make sure you saw the Cancer Data Science Slack, which you are welcome to join for more informal communication. Feel free to DM me there or ask question in the #open-scpca channel there!

[jashapiro]

Seems like a few extra (mostly empty) files snuck in here: 1.7, =2.15, =2.5 =3.6

[jashapiro]

This looks like something went wrong with the conda setup? Are you planning to use conda in this module? If not (or not yet), you can probably just remove this for now.