Merge pull request #45 from broadinstitute/shntnu-patch-1

Add everything but the license for now

README.md

@@ -1,13 +1,17 @@
-# Processed Cell Painting Data for the LINCS Drug Repurposing Project
+# Processed Data for the LINCS Cell Painting Project
 
-The repository stores data and data processing scripts for **a subset** of the LINCS Drug Repurposing Project.
-In this project, we perturbed A549 cells with ~1,500 compounds across 6 doses with ~4 biological replicates.
+The repository stores data and data processing scripts for **a subset** of the [Broad Drug Repurposing Hub](https://clue.io/repurposing#home) collection of compounds.
 
-For a specific list of compounds tested, see [`metadata`](https://github.com/broadinstitute/lincs-cell-painting/tree/master/metadata).
+In this project, the [Connectivity Map](https://clue.io/team) team perturbed A549 cells with ~1,500 compounds across 6 doses in 5 technical replicates. 
+We refer to this dataset as `LINCS Pilot 1`.
+
+For a specific list of compounds tested, see [`metadata`](https://github.com/broadinstitute/lincs-cell-painting/tree/master/metadata). 
+Information about the compounds can be interactively explored in the [CLUE Repurposing app](https://clue.io/repurposing-app). 
+The [Morphology Connectivity Hub](https://clue.io/morphology) is the primary source of this dataset.
 
 ## Image-Based Profiling
 
-We apply a unified, image-based profiling pipeline to all Drug Repurposing Hub Cell Painting plates.
+We apply a unified, image-based profiling pipeline to all 136 384-well plates from `LINCS Pilot 1` .
 We use [pycytominer](https://github.com/cytomining/pycytominer) as the primary tool for image-based profiling.
 
 The profiles are processed and stored in the [profiles/](profiles/) directory.