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Jamboree dimensionality reduction metrics #317

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merged 20 commits into from
Mar 16, 2022

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@lazappi lazappi commented May 14, 2021

Submission type

  • This submission adds a new dataset
  • This submission adds a new method
  • This submission adds a new metric
  • This submission adds a new task
  • This submission adds a new Docker image
  • This submission fixes a bug (link to related issue: )
  • This submission adds a new feature not listed above

Testing

  • This submission was written on a forked copy of SingleCellOpenProblems
  • GitHub Actions "Run Benchmark" tests are passing on this base branch of this pull request (include link to passed test: )
  • If this pull request is not ready for review (including passing the "Run Benchmark" tests), I will open this PR as a draft (click on the down arrow next to the "Create Pull Request" button)

Submission guidelines

  • This submission follows the guidelines in our Contributing document
  • I have checked to ensure there aren't other open Pull Requests for the same update/change

PR review checklist

This PR will be evaluated on the basis of the following checks:

  • The task addresses a valid open problem in single-cell analysis
  • The latest version of master is merged and tested
  • The methods/metrics are imported to __init__.py and were tested in the pipeline
  • Method and metric decorators are annotated with paper title, year, author, code version, and date
  • The README gives an outline of the methods, metrics and datasets in the folder
  • The README provides a satisfactory task explanation (for new tasks)
  • The sample test data is appropriate to test implementation of all methods and metrics (for new tasks)

Description

This PR contains the following new dimensionality reduction metrics from the jamboree:

Metric Author Issue Original PR
NN co-ranking @michalk8 #300 lazappi/pull/8
Local density @michalk8 #291 lazappi/pull/7

michalk8 and others added 19 commits March 31, 2021 14:26
* master:
  Update alra.py
  Update alra.R
  pre-commit
  Create alra.R
  pre-commit
  Update alra.py
  make var names unique for tenx data loader
  Force docker_build on `master`
  Dockerfile bugfix
  Update CONTRIBUTING.md
  Update README.md
  Create alra.py
  Delete alra.py
  Create alra.py
* master:
  fix region
  fix nf wkdir
  use env.BRANCH
  rm echo
  BRANCH -> WKDIR for s3
  set branch variable in S3 setup job
  Fix s3 bucket clash
  Dimred methods preprocessing (openproblems-bio#301)
  Add trustworthiness score for dimred task (openproblems-bio#258)
  Add Method SCOT to Multi-modal data Integration Task (openproblems-bio#298)
  Update README.md
  Update README.md
  Update README.md
* master:
  Update alra.py (openproblems-bio#304)
  updated template for PR with PR evaluation checks (openproblems-bio#314)
@mvinyard mvinyard self-requested a review May 28, 2021 19:32
@mvinyard mvinyard requested a review from LuckyMD May 28, 2021 19:35
@scottgigante-immunai scottgigante-immunai merged commit 9ea9416 into openproblems-bio:main Mar 16, 2022
lazappi added a commit to lazappi/openproblems that referenced this pull request Mar 24, 2022
* upstream/main:
  Convert normalizers to return anndata (openproblems-bio#329)
  require anndata<0.8 (openproblems-bio#336)
  Fix GPG key for R install (openproblems-bio#334)
  Fix R dependencies for docker build (openproblems-bio#331)
  Jamboree dimensionality reduction datasets (openproblems-bio#316)
  Jamboree dimensionality reduction metrics (openproblems-bio#317)
  use cmake==3.18.4 for multicoretsne build (openproblems-bio#328)
  Update 'master' to 'main' on CI (openproblems-bio#326)
  New key breaks r docker container build (openproblems-bio#322)
@lazappi lazappi deleted the dimred-metrics branch April 11, 2022 08:48
rcannood added a commit that referenced this pull request Sep 4, 2024
* remove multimodal starter dataset

* fix indentation

---------

Co-authored-by: Robrecht Cannoodt <[email protected]>
rcannood added a commit that referenced this pull request Sep 4, 2024
* remove multimodal starter dataset

* fix indentation

---------

Co-authored-by: Robrecht Cannoodt <[email protected]>
Former-commit-id: 2cf2a73
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4 participants