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added filter for truth annotations to support CellProfiler benchmarking #95

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Merged
okraus merged 2 commits into from
Jan 28, 2025
Merged

added filter for truth annotations to support CellProfiler benchmarking #95

okraus merged 2 commits into from
Jan 28, 2025

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@okraus okraus commented Jan 21, 2025

What?

  • added line to filter gene_symbol and treatment from the truth dataframe to only whats in the map_data.metadata.perturbation column

Why?

  • Unfortunately our CellProfiler processing is missing a bunch of wells from the original dataset, so we need to apply these filters. Some stats:
CellProfiler_filter has 184,492 out of 222,601 original wells
CellProfiler_filter has 2080 out of 2921 relationships - missing 841 relationships
CellProfiler_filter has 1190 of 1674 compounds
CellProfiler_filter has 721 of 736 genes

@okraus okraus requested a review from safiyecelik as a code owner January 21, 2025 04:40
@okraus okraus merged commit 60df3eb into trunk Jan 28, 2025
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@okraus okraus deleted the fix_for_cellprofiler_metadata branch January 28, 2025 02:48
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@safiyecelik safiyecelik safiyecelik approved these changes

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@okraus @safiyecelik @kian-kd @fedecomitani