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Merge test#1

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arl94 wants to merge 43 commits into
arl94:method-add-predicting-chromatin-gexfrom
openproblems-bio:master
Open

Merge test#1
arl94 wants to merge 43 commits into
arl94:method-add-predicting-chromatin-gexfrom
openproblems-bio:master

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@arl94 arl94 commented Mar 29, 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

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  • 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)

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  • 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

wes-lewis and others added 6 commits March 29, 2021 09:07
Add alra.py file as created previously from the wrong branch.
removing from the incorrect task
Add alra to denoising task
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arl94 commented Mar 29, 2021

Test merge with my fork

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codecov-io commented Mar 30, 2021

Codecov Report

❗ No coverage uploaded for pull request base (method-add-predicting-chromatin-gex@6131a45). Click here to learn what that means.
The diff coverage is n/a.

Impacted file tree graph

@@                          Coverage Diff                           @@
##             method-add-predicting-chromatin-gex       #1   +/-   ##
======================================================================
  Coverage                                       ?   89.11%           
======================================================================
  Files                                          ?       73           
  Lines                                          ?     1498           
  Branches                                       ?       90           
======================================================================
  Hits                                           ?     1335           
  Misses                                         ?      134           
  Partials                                       ?       29           
Flag Coverage Δ
unittests 89.11% <0.00%> (?)

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dburkhardt and others added 14 commits March 31, 2021 10:27
* Add SCOT method to multimodal data integration task

* pre-commit

* Fix flake things

* pre-commit

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* Add trustworthiness score

* Address comments, add test

* Fix test

* Update README.md

* Update README.md

* Update README.md

* Update README.md

Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com>
* Add preprocessing.py for dim red methods

This file should contain standard pre-processing functions used to
create variations on different methods

* Add pre-processing function existing dim red methods

Create a new PHATE variant using Scanpy pre-processing

* Update dim red README to describe pre-processing

* pre-commit

* Pre-commit fixes

* Move PHATE import inside function

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com>
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codecov-commenter commented Apr 21, 2021

Codecov Report

❗ No coverage uploaded for pull request base (method-add-predicting-chromatin-gex@6131a45). Click here to learn what that means.
The diff coverage is n/a.

Impacted file tree graph

@@                          Coverage Diff                           @@
##             method-add-predicting-chromatin-gex       #1   +/-   ##
======================================================================
  Coverage                                       ?   89.30%           
======================================================================
  Files                                          ?       73           
  Lines                                          ?     1533           
  Branches                                       ?       90           
======================================================================
  Hits                                           ?     1369           
  Misses                                         ?      135           
  Partials                                       ?       29           
Flag Coverage Δ
unittests 89.30% <0.00%> (?)

Flags with carried forward coverage won't be shown. Click here to find out more.


Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 6131a45...3c6956b. Read the comment docs.

* Update alra.py

Fix pre-processing and transformation back into the original space

* pre-commit

* Update alra.py


* make sure necessary methods are imported


Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com>
@dburkhardt dburkhardt deleted the master branch May 21, 2021 17:25
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