v0.4.4

.gitignore

@@ -158,3 +158,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+examples/data/
+.vscode/

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2024, Broad Institute
+Copyright (c) 2025, Broad Institute
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

README.md

@@ -39,8 +39,9 @@ pytest
 
 We provide examples demonstrating how to use copairs for:
 - [grouping profiles based on their metadata](./examples/finding_pairs.ipynb)
-- [calculating mAP to assess phenotypic activity and consistnecy of perturbation using real data](./examples/mAP_demo.ipynb)
-
+- [calculating mAP to assess phenotypic activity of perturbations](./examples/phenotypic_activity.ipynb)
+- [calculating mAP to assess phenotypic consistency of perturbations](./examples/phenotypic_consistency.ipynb)
+- [estimating null size for mAP p-value calculation](./examples/null_size.ipynb)
 
 ## Citation
 If you find this work useful for your research, please cite our [pre-print](https://doi.org/10.1101/2024.04.01.587631):

examples/README.md

@@ -0,0 +1,32 @@
+ # Examples
+
+Example notebooks demostrating the use of `copairs`.
+
+## Installation
+
+To install dependencies for running examples, run:
+```bash
+pip install copairs[demo]
+```
+
+## Running examples
+
+```bash
+cd examples
+notebook
+```
+
+## List of examples
+
+We show how to use copairs for:
+
+- [grouping profiles based on their metadata](./finding_pairs.ipynb)
+- [calculating mAP to assess phenotypic activity of perturbations](./phenotypic_activity.ipynb)
+- [calculating mAP to assess phenotypic consistency of perturbations](./phenotypic_consistency.ipynb)
+- [estimating null size for mAP p-value calculation](./null_size.ipynb)
+
+## Data used
+
+In these examples, we used a single plate of profiles from the dataset "cpg0004" (aka LINCS), which contains Cell Painting images of 1,327 small-molecule perturbations of A549 human cells. The wells on each plate were perturbed with 56 different compounds in six different doses.
+
+> Way, G. P. et al. Morphology and gene expression profiling provide complementary information for mapping cell state. Cell Syst 13, 911–923.e9 (2022).

examples/finding_pairs.ipynb

@@ -107,7 +107,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -278,7 +278,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "map_benchmark",
+   "display_name": "copairs",
    "language": "python",
    "name": "python3"
   },
@@ -292,7 +292,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.9.19"
   }
  },
  "nbformat": 4,