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Test PCA and scVI on genome-wide data #24

Merged
merged 15 commits into from
Nov 14, 2023
Merged

Test PCA and scVI on genome-wide data #24

merged 15 commits into from
Nov 14, 2023

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safiyecelik
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What?

  • make sure we can run PCA and scVI on genome-wide data

Why?

  • because we want to build genome-wide maps

safiyecelik and others added 14 commits October 29, 2023 14:28
@safiyecelik
convert string to Path in reading benchmark data
e5f0a0c
@safiyecelik
Merge branch 'trunk' into clean_jump_notebook
09127c4
@safiyecelik
simple jump notebook
2cea4b8
@safiyecelik
fix perturbation column
99d229f
@safiyecelik
separate filtering from data loading
3f4426c
@safiyecelik
fix median syntax
967d6ba
@safiyecelik @dependabot
Bump pyarrow from 13.0.0 to 14.0.1 in /requirements (#22) (#23)
48c0593 
Bumps [pyarrow](https://github.com/apache/arrow) from 13.0.0 to 14.0.1.
- [Commits](apache/arrow@go/v13.0.0...apache-arrow-14.0.1)

---
updated-dependencies:
- dependency-name: pyarrow
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@safiyecelik
add no scaling option to align_on_controls
e26dbd3
@safiyecelik
update docstring and delete the jump metadata files
70f3bb8
@safiyecelik
convert read_parquet function to lambda function
80c23f0
@safiyecelik
take care of nans
b345b2a
@safiyecelik
remove genes w/ nan or inf values
cf870cd
@safiyecelik
remove genes w/ nan or inf values
9279e34
@safiyecelik
fix_data_link
0ffeff9
@safiyecelik safiyecelik requested a review from a team as a code owner November 13, 2023 19:03
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@safiyecelik safiyecelik merged commit 6083660 into trunk Nov 14, 2023
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@safiyecelik safiyecelik deleted the full_data_runs branch November 14, 2023 23:16
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@ctilling ctilling ctilling approved these changes

@kr-hansen kr-hansen Awaiting requested review from kr-hansen kr-hansen was automatically assigned from recursionpharma/cartography

@wpbone wpbone Awaiting requested review from wpbone wpbone was automatically assigned from recursionpharma/cartography

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@safiyecelik @ctilling