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Feature/254 Add TF-gene correlations to the SCENIC GRN output #257

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merged 2 commits into from
Nov 27, 2020
Merged

Feature/254 Add TF-gene correlations to the SCENIC GRN output #257

merged 2 commits into from
Nov 27, 2020

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cflerin
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@cflerin cflerin commented Nov 24, 2020

Add TF-gene correlations to the SCENIC GRN output:

  • Update pySCENIC to 0.10.4
  • Use the pyscenic add_cor command to add Pearson correlations for each TF-gene pair in the GRN output file, write this to a new file, which is published with the SCENIC output files.
  • Fixes Adding correlation to GRNBoost adjency table #254

@cflerin
Relink scenic module to add GRN correlations step
621aad9 
- Update to pySCENIC 0.10.4
- GRN output with correlations is now published to the scenic output
location
- Fixes #254
@cflerin cflerin requested review from dweemx and KrisDavie November 24, 2020 14:10
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dweemx approved these changes Nov 24, 2020
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Approved but would be nice to have more explicit variable names/process names for

  • grn_wCor (e.g.: grn_with_correlation)
  • ADD_COR (e.g.: ADD_CORRELATION or ADD_SPEARMAN_CORRELATION if this one is calculated)

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cflerin commented Nov 24, 2020

  • grn_wCor (e.g.: grn_with_correlation)
  • ADD_COR (e.g.: ADD_CORRELATION or ADD_SPEARMAN_CORRELATION if this one is calculated)

Thanks, made these changes in the last commit

@cflerin cflerin merged commit 0edf4ae into develop Nov 27, 2020
@cflerin cflerin deleted the feature/254-add_scenic_grn_cor branch November 27, 2020 13:41
@cflerin cflerin mentioned this pull request Dec 1, 2020
Merged
KrisDavie pushed a commit that referenced this pull request Dec 8, 2020
@cflerin
Merge pull request #257 from vib-singlecell-nf/feature/254-add_scenic…
badb9f7 
…_grn_cor

Feature/254 Add TF-gene correlations to the SCENIC GRN output

Former-commit-id: 0edf4ae
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@dweemx dweemx dweemx approved these changes

@KrisDavie KrisDavie Awaiting requested review from KrisDavie

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