lincs-cell-painting

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use the [`cytominer-eval` library](https://github.com/cytomining/cytominer-eval). An example https://github.com/jump-cellpainting/develop-computational-pipeline/issues/4#issuecomment-693006903 is pasted below: After installing with: ```bash pip install git+https://github.com/cytomining/cytominer-eval@56bd9e545d4ce5dea8c2d3897024a4eb241d06db ``` This now works: ```python import pandas as pd from cytominer_eval import evaluate...

gwaybio

While working on CPJUMP-Stain2, @shntnu and I [observed](https://github.com/jump-cellpainting/pilot-analysis/issues/15#issuecomment-675754131) that the proportion of compounds with a strong signal (percent strong metric) was similar if the analysis was performed with individual channels...

niranjchandrasekaran

Plate causing numerical issues

1

In the [cell health](https://github.com/broadinstitute/cell-health) project, I noticed some strange behavior with a specific plate. The plate is `SQ00015221` coming from plate map `C-7161-01-LM6-011`. The offending features seem to be based...

gwaybio

Currently, all profiles are normalized [based on `mad_robustize`](https://github.com/broadinstitute/lincs-cell-painting/blob/master/profiles/profile.py#L37). We can use this repository to systematically evaluate if one strategy is better. ## Rationale As noted in https://github.com/broadinstitute/lincs-cell-painting/issues/4#issuecomment-620978559 >> The default...

gwaybio

How do updated moa/target annotations influence moa/target recall?

1

A potentially fun analysis would be to evaluate how the different moa/target annotations updated over time (in different CLUE drugs/samples versions) influence moa/target recall. Essentially, we would setup an eval...

gwaybio