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02 run azimuth before kweight #737
02 run azimuth before kweight #737
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Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Uncomment workflow triggers, download relevant project, and run workflow
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…terize_fetal_kidney_reference_Stewart.Rmd Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…transfer_fetal_kidney_reference_Stewart.Rmd Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…transfer_fetal_kidney_reference_Stewart.Rmd Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…terize_fetal_kidney_reference_Stewart.Rmd Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…fetal-kidney-ref.R Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…processing.Rmd Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…transfer_fetal_full_reference_Cao.Rmd Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Thank you very much @jaclyn-taroni ! I'll do the last changes on the Thank you so much, looking forward the next steps :D |
@jaclyn-taroni FYI, the extraneous RDS files for samples 168-178 in my results bucket should have been removed using --destructive-sync ! |
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Thanks for the updates, @maud-p! I am going to approve at this time 👍🏻
There are a couple things that will make future PRs easier until we figure out how to approach testing the Azimuth notebooks. I will make those changes here and then get this merged in! 🥳
…d-p/OpenScPCA-analysis into 02_RunAzimuth_before_kweight
5afefe3 is just the HTML output of the notebooks after the change in 7e877ed, which passed CI: https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/runs/10656117562/job/29534402700 Merging without the check on running the module. |
Thank you so much @jaclyn-taroni ! It is great to see the merge in the main branch :) I'll create a new branch from here and continue with PR #704 ! Thanks!! |
Purpose/implementation Section
Please link to the GitHub issue that this pull request addresses.
Copying the PR#706 #706 to:
• roll back to what we had in f98da21? (i.e., before all the k.weight debugging, etc.)
• use system() instead of source() for download-and-create-fetal-kidney-ref.R in 00_run_workflow.R
#703
What is the goal of this pull request?
I write a RMarkdown script to
This will be used in the module to perform label transfer from the human fetal kidney atlas to the Wilms tumor samples.
Briefly describe the general approach you took to achieve this goal.
I used a different approach than described in the issue #703 .
I figured out that I can download the human fetal kidney data from cellxgene as a rds object.
url = "https://datasets.cellxgene.cziscience.com/40ebb8e4-1a25-4a33-b8ff-02d1156e4e9b.rds"
Like this, I didn't need to create a conda/renv enrironment.
The dockerfile from this PR is the same as the dockerfile from the PR #704 .
Of note however, using your documentation, I have been able to build a conda/renv container that actually allow to run the scripts I did so far, in case we need it in the future :)
If known, do you anticipate filing additional pull requests to complete this analysis module?
Yes! The next one will be to implement the label transfer in the sample report.
Results
What is the name of your results bucket on S3?
here is the command I used to upload the result to the bucket:
What types of results does your code produce (e.g., table, figure)?
The azimuth compatible reference in a format of 2 files:
When running the 00_fetal_reference_kidney.Rmd, these two files will be saved in the module folder/marker-genes.
What is your summary of the results?
We build a reference that is compatible with the azimuth label transfer.
Provide directions for reviewers
I have one issue, using the RMarkdown 00_fetal_reference_kidney.Rmd, we can only build the reference manually running each chunk, but it do not work when we want to knittr as html report.
I could isolate the problem to the AzimuthReference function, might be related to this issue: satijalab/azimuth#219
What are the software and computational requirements needed to be able to run the code in this PR?
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
README.md
has been updated to reflect code changes in this pull request.Reproducibility checklist
Dockerfile
.environment.yml
file.renv.lock
file.