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broadinstitute / lincs-cell-painting

Processed Cell Painting Data for the LINCS Drug Repurposing Project
BSD 3-Clause "New" or "Revised" License
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Second batch of lincs data #57

Closed gwaybio closed 3 years ago

gwaybio commented 3 years ago

@shntnu - I remember you mentioning that we have another batch of Cell Painting data for this project. Can you point me to where this data lives?

We should work towards getting this data on here and processed. @sMyn42 is looking for a good dataset to test different batch effect correction tools (e.g. Harmony) to extend his Summer Research project. Having the second batch on here will help!

shntnu commented 3 years ago

The backends are at https://imaging-platform-cold.s3.us-east-1.amazonaws.com/imaging_analysis/2015_10_05_DrugRepurposing_AravindSubramanian_GolubLab_Broad/plates/2015_10_05_DrugRepurposing_AravindSubramanian_GolubLab_Broad_2017_12_05_Batch2_*_backend.tar.gz

Here's how you'd restore them https://github.com/broadinstitute/imaging-backup-scripts/blob/master/glacier_restore.md

Here's the description of this data set https://docs.google.com/document/d/1KA4j_grc1uxkCdhCzqEQSps8MGZf9NT7V_F8mmEwPGw/edit

gwaybio commented 3 years ago

PROJECT_NAME=2015_10_05_DrugRepurposing_AravindSubramanian_GolubLab_Broad BATCH_ID=2017_12_05_Batch2

gwaybio commented 3 years ago

list_of_plates.txt

gwaybio commented 3 years ago

batch 2 sqlite files now available internally at /home/ubuntu/bucket/projects/2015_10_05_DrugRepurposing_AravindSubramanian_GolubLab_Broad/workspace/backend/2017_12_05_Batch2

gwaybio commented 3 years ago

I added batch 2 data in #58 - We can also perform some sort of check, a quick dataset description, and add the results to https://github.com/broadinstitute/lincs-cell-painting/tree/master/comparison

sMyn42 commented 3 years ago

Cool! I'm planning to get back at it this weekend.

On Mon, Feb 22, 2021 at 1:09 PM Greg Way notifications@github.com wrote:

I added batch 2 data in #58 https://github.com/broadinstitute/lincs-cell-painting/pull/58 - We can also perform some sort of check, a quick dataset description, and add the results to https://github.com/broadinstitute/lincs-cell-painting/tree/master/comparison

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gwaybio commented 3 years ago

58 only contains well profiles (levels 2-4b) - We also need to create consensus signatures (level 5) for batch 2 data

gwaybio commented 3 years ago

Creating batch 2 consensus signatures in #61

gwaybio commented 3 years ago

the second batch of LINCS data lacks several MOA/Target annotations in our existing metadata map.

We're troubleshooting this in https://github.com/broadinstitute/lincs-cell-painting/issues/62#issuecomment-812184977

gwaybio commented 3 years ago

I just started running the full profiling pipeline on both batches of data

gwaybio commented 3 years ago

full pipeline is complete, and now frozen, after merging #63