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adding IDR files #81

Merged
merged 2 commits into from
Oct 27, 2021
Merged

adding IDR files #81

merged 2 commits into from
Oct 27, 2021

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tnat1031
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@shntnu here is the code and input files for making the library file for submission to IDR. The IDR submission files are in this shared google folder: https://drive.google.com/drive/folders/1t_P4FgaSj9c4nxmIrydqArvCumhFWbCC?usp=sharing

@shntnu
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shntnu commented Oct 26, 2021

This is great! Thanks @tnat1031

  1. For the study file: is the txt file identical to the sheet here https://drive.google.com/drive/folders/1NF6PeJ6oz_TneIdEQk_payB8F-zyls6k? If so, I'll delete the txt file to avoid any confusion
  2. Please move the idr folder to live under metadata
  3. Is the file https://github.com/cmap/lincs-cell-painting/blob/master/idr/2016_04_01_a549_48hr_batch1_metadata_cell_count_summary.tsv the same as https://github.com/cmap/lincs-cell-painting/blob/master/profiles/cell_count/2016_04_01_a549_48hr_batch1_metadata_cell_count_summary.tsv.gz?

@tnat1031
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Sure thing @shntnu.

  1. Yes, those files are identical so feel free to delete the .txt.
  2. I have moved the idr folder under metadata
  3. Yes those files are the same

# sample meta from L1000 (may not really need this)
# sample_meta_l1k <- fread("col_meta_level_3_n421176.txt")
# same from cp
sample_meta_cp <- fread("2016_04_01_a549_48hr_batch1_metadata_cell_count_summary.tsv")
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@shntnu
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shntnu commented Oct 27, 2021

Thanks @tnat1031

(you can ignore the last comment; I'll take it from here)

@shntnu shntnu merged commit 3c27be5 into broadinstitute:master Oct 27, 2021
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2 participants