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29 changes: 29 additions & 0 deletions LICENSE_BSD3.md
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# BSD 3-Clause License

_Copyright (c) 2020, The Broad Institute of MIT and Harvard_
_All rights reserved._

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.

* Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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121 changes: 121 additions & 0 deletions LICENSE_CC0.md
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# Creative Commons Legal Code

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24 changes: 17 additions & 7 deletions README.md
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# Processed Data for the LINCS Cell Painting Project
# LINCS Cell Painting profile data repository

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.
The Library of Integrated Network-Based Cellular Signatures (LINCS) Project aims to create publicly available resources to characterize how cells respond to perturbation.
This repository stores Cell Painting readouts and associated data-processing pipelines for the LINCS Cell Painting dataset.

In this project, the [Connectivity Map](https://clue.io/team) team perturbed A549 cells with 1,571 compounds across 6 doses in 5 technical replicates.
The data represent **a subset** of the [Broad Drug Repurposing Hub](https://clue.io/repurposing#home) collection of compounds.

We refer to this dataset as `LINCS Pilot 1`.
We also include data for the second batch of LINCS Cell Painting data, which we refer to as `LKCP`.

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).
You can interactively explore information about the compounds 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
## Image-based profiling

We apply a unified, image-based profiling pipeline to all 136 384-well plates from `LINCS Pilot 1` .
We apply a unified, image-based profiling pipeline to all 136 384-well plates from `LINCS Pilot 1`, and all 135 384-well plates from `LKCP`.
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.
We process and store profiles in the [profiles/](profiles/) directory.
See [`profiles/README.md`](profiles/README.md) for more details and for instructions on how to reproduce the pipeline.

For more details about image-based profiling in general, please refer to [Caicedo et al. 2017](https://doi.org/10.1038/nmeth.4397).

## Computational Environment
## Computational environment

We use [conda](https://docs.conda.io/en/latest/) to manage the computational environment.

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```

Also note that when contributing to the repository, make sure to add any new package in the `environment.yml` file.

## License

We use a dual license in this repository.
We license the source code as [BSD 3-Clause](LICENSE_BSD3.md), and license the data, results, and figures as [CC0 1.0](LICENSE_CC0.md).
136 changes: 136 additions & 0 deletions metadata/platemaps/2017_12_05_Batch2/barcode_platemap.csv
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Assay_Plate_Barcode,Plate_Map_Name
BR00092655,LKCP001_A549_6H
BR00092656,LKCP001_A549_6H
BR00092657,LKCP001_A549_6H
BR00092658,LKCP001_A549_6H
BR00092659,LKCP001_A549_6H
BR00092660,LKCP002_A549_6H
BR00092661,LKCP002_A549_6H
BR00092662,LKCP002_A549_6H
BR00092663,LKCP002_A549_6H
BR00092664,LKCP002_A549_6H
BR00092665,ASG003_A549_6H
BR00092666,ASG003_A549_6H
BR00092667,ASG003_A549_6H
BR00092668,ASG003_A549_6H
BR00092669,ASG003_A549_6H
BR00092670,LKCP001_MCF7_6H
BR00092671,LKCP001_MCF7_6H
BR00092672,LKCP001_MCF7_6H
BR00092673,LKCP001_MCF7_6H
BR00092674,LKCP001_MCF7_6H
BR00092675,LKCP002_MCF7_6H
BR00092676,LKCP002_MCF7_6H
BR00092677,LKCP002_MCF7_6H
BR00092678,LKCP002_MCF7_6H
BR00092679,LKCP002_MCF7_6H
BR00092680,ASG003_MCF7_6H
BR00092681,ASG003_MCF7_6H
BR00092682,ASG003_MCF7_6H
BR00092683,ASG003_MCF7_6H
BR00092684,ASG003_MCF7_6H
BR00092685,LKCP001_U2OS_6H
BR00092686,LKCP001_U2OS_6H
BR00092687,LKCP001_U2OS_6H
BR00092688,LKCP001_U2OS_6H
BR00092689,LKCP001_U2OS_6H
BR00092690,LKCP002_U2OS_6H
BR00092691,LKCP002_U2OS_6H
BR00092692,LKCP002_U2OS_6H
BR00092693,LKCP002_U2OS_6H
BR00092694,LKCP002_U2OS_6H
BR00092695,ASG003_U2OS_6H
BR00092696,ASG003_U2OS_6H
BR00092697,ASG003_U2OS_6H
BR00092698,ASG003_U2OS_6H
BR00092699,ASG003_U2OS_6H
BR00092700,LKCP001_A549_24H
BR00092701,LKCP001_A549_24H
BR00092702,LKCP001_A549_24H
BR00092703,LKCP001_A549_24H
BR00092704,LKCP001_A549_24H
BR00092705,LKCP002_A549_24H
BR00092706,LKCP002_A549_24H
BR00092707,LKCP002_A549_24H
BR00092708,LKCP002_A549_24H
BR00092709,LKCP002_A549_24H
BR00092710,ASG003_A549_24H
BR00092711,ASG003_A549_24H
BR00092712,ASG003_A549_24H
BR00092713,ASG003_A549_24H
BR00092714,ASG003_A549_24H
BR00092715,LKCP001_MCF7_24H
BR00092716,LKCP001_MCF7_24H
BR00092717,LKCP001_MCF7_24H
BR00092718,LKCP001_MCF7_24H
BR00092719,LKCP001_MCF7_24H
BR00092720,LKCP002_MCF7_24H
BR00092721,LKCP002_MCF7_24H
BR00092722,LKCP002_MCF7_24H
BR00092723,LKCP002_MCF7_24H
BR00092724,LKCP002_MCF7_24H
BR00092725,ASG003_MCF7_24H
BR00092726,ASG003_MCF7_24H
BR00092727,ASG003_MCF7_24H
BR00092728,ASG003_MCF7_24H
BR00092729,ASG003_MCF7_24H
BR00092730,LKCP001_U2OS_24H
BR00092731,LKCP001_U2OS_24H
BR00092732,LKCP001_U2OS_24H
BR00092733,LKCP001_U2OS_24H
BR00092734,LKCP001_U2OS_24H
BR00092735,LKCP002_U2OS_24H
BR00092736,LKCP002_U2OS_24H
BR00092737,LKCP002_U2OS_24H
BR00092738,LKCP002_U2OS_24H
BR00092739,LKCP002_U2OS_24H
BR00092740,ASG003_U2OS_24H
BR00092741,ASG003_U2OS_24H
BR00092742,ASG003_U2OS_24H
BR00092743,ASG003_U2OS_24H
BR00092744,ASG003_U2OS_24H
BR00092745,LKCP001_A549_48H
BR00092746,LKCP001_A549_48H
BR00092747,LKCP001_A549_48H
BR00092748,LKCP001_A549_48H
BR00092749,LKCP001_A549_48H
BR00092750,LKCP002_A549_48H
BR00092751,LKCP002_A549_48H
BR00092752,LKCP002_A549_48H
BR00092753,LKCP002_A549_48H
BR00092754,LKCP002_A549_48H
BR00092755,ASG003_A549_48H
BR00092756,ASG003_A549_48H
BR00092757,ASG003_A549_48H
BR00092758,ASG003_A549_48H
BR00092759,ASG003_A549_48H
BR00092760,LKCP001_MCF7_48H
BR00092761,LKCP001_MCF7_48H
BR00092762,LKCP001_MCF7_48H
BR00092763,LKCP001_MCF7_48H
BR00092764,LKCP001_MCF7_48H
BR00092765,LKCP002_MCF7_48H
BR00092766,LKCP002_MCF7_48H
BR00092767,LKCP002_MCF7_48H
BR00092768,LKCP002_MCF7_48H
BR00092769,LKCP002_MCF7_48H
BR00092770,ASG003_MCF7_48H
BR00092771,ASG003_MCF7_48H
BR00092772,ASG003_MCF7_48H
BR00092773,ASG003_MCF7_48H
BR00092774,ASG003_MCF7_48H
BR00092775,LKCP001_U2OS_48H
BR00092776,LKCP001_U2OS_48H
BR00092777,LKCP001_U2OS_48H
BR00092778,LKCP001_U2OS_48H
BR00092779,LKCP001_U2OS_48H
BR00092780,LKCP002_U2OS_48H
BR00092781,LKCP002_U2OS_48H
BR00092782,LKCP002_U2OS_48H
BR00092783,LKCP002_U2OS_48H
BR00092784,LKCP002_U2OS_48H
BR00092785,ASG003_U2OS_48H
BR00092786,ASG003_U2OS_48H
BR00092787,ASG003_U2OS_48H
BR00092788,ASG003_U2OS_48H
BR00092789,ASG003_U2OS_48H
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