lincs-cell-painting
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broadinstitute
Processed Cell Painting Data for the LINCS Drug Repurposing Project
We will upload image files to the [Image Data Resource](https://idr.openmicroscopy.org/) and add URL and metadata information to the [Broad Bioimage Benchmark Collection](https://data.broadinstitute.org/bbbc/). We will use this issue to outline the...
Hi, I work for ViQi Inc. and I've been exploring jump datasets to run our AI-based image analysis on. We'd like to work with your dataset and I have a...
Juan asked this: I need to process the LINCS dataset to proceed with the plan we discussed for LUAD. I'm going to need access to the images, which is a...
@EchteRobert reported this: Q about the LINCS dataset: I have run into plates which contain slightly fewer measured features than the bulk of the plates, i.e., 1745 instead of 1781....
Hi @gwaybio I see that single cell profiles are not included in this repo. Where can I find the single cell locations? Is it on an S3 bucket somewhere? Thanks!
In #73 @michaelbornholdt fixed the workflow diagram for processing the LINCS cell painting profiles. We have since realized that this workflow diagram is incorrect. @michaelbornholdt - are you able to...
This is a reminder to tackle soon. I don't know what I am doing wrong but when I download some non spherized consensus data and run enrichment over it. The...
The [spherize notebook](https://github.com/broadinstitute/lincs-cell-painting/blob/e9737c3e4e4443eb03c2c278a145f12efe255756/spherized_profiles/0.spherize-batch-effects.ipynb) documentation should be improved. @shntnu notes in #60 The notebook says > Here, we load in all normalized profiles (level 4a) data across all plates and apply...
@FloHu noticed that the original names of the features are carried through after spherizing. We might want to not do that since it can confuse people actually using the consensus...
It is very useful for researchers to be able to browse a heat map with a dendrogram attached (or some other representation - it's hard!) and look at relationships among...
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Processed Cell Painting Data for the LINCS Drug Repurposing Project