ScreenPro2 0.6.1__tar.gz → 0.7.0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (25) hide show
  1. {screenpro2-0.6.1 → screenpro2-0.7.0}/PKG-INFO +10 -7
  2. {screenpro2-0.6.1 → screenpro2-0.7.0}/README.md +9 -6
  3. {screenpro2-0.6.1 → screenpro2-0.7.0}/pyproject.toml +1 -1
  4. {screenpro2-0.6.1 → screenpro2-0.7.0}/LICENSE +0 -0
  5. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/__init__.py +0 -0
  6. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/__main__.py +0 -0
  7. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/assays/__init__.py +0 -0
  8. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/dashboard/__init__.py +0 -0
  9. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/load.py +0 -0
  10. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/main.py +0 -0
  11. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/ngs/__init__.py +0 -0
  12. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/ngs/cas12.py +0 -0
  13. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/ngs/cas9.py +0 -0
  14. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/phenoscore/__init__.py +0 -0
  15. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/phenoscore/_annotate.py +0 -0
  16. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/phenoscore/delta.py +0 -0
  17. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/phenoscore/deseq.py +0 -0
  18. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/phenoscore/evaluate.py +0 -0
  19. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/phenoscore/phenostat.py +0 -0
  20. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/plotting/__init__.py +0 -0
  21. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/plotting/_rank.py +0 -0
  22. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/plotting/_utils.py +0 -0
  23. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/plotting/pheno_plots.py +0 -0
  24. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/plotting/qc_plots.py +0 -0
  25. {screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/preprocessing.py +0 -0
{screenpro2-0.6.1 → screenpro2-0.7.0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: ScreenPro2
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- Version: 0.6.1
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+ Version: 0.7.0
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  Summary: Flexible analysis of high-content CRISPR screening
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  License: MIT
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  License-File: LICENSE
@@ -21,7 +21,8 @@ Project-URL: Repository, https://github.com/ArcInstitute/ScreenPro2
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  Description-Content-Type: text/markdown
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  [![website](https://img.shields.io/badge/website-live-brightgreen)](https://arcinstitute.org/tools/screenpro2)
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- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18807934.svg)](https://doi.org/10.5281/zenodo.18807934)
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+ [![zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.18807934.svg)](https://doi.org/10.5281/zenodo.18807934)
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+ [![NCB](https://img.shields.io/badge/DOI-10.1038%2Fs41589--026--02312--z-blue.svg)](https://doi.org/10.1038/s41589-026-02312-z)
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  [![PyPI version](https://badge.fury.io/py/ScreenPro2.svg)](https://badge.fury.io/py/ScreenPro2)
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  [![Documentation Status](https://readthedocs.org/projects/screenpro2/badge/?version=latest)](https://screenpro2.readthedocs.io/en/latest/?version=latest)
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  [![Downloads](https://static.pepy.tech/badge/screenpro2)](https://pepy.tech/project/screenpro2)
@@ -359,11 +360,13 @@ ScreenPro2 is licensed under the terms of the MIT license (see [LICENSE](LICENSE
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  by Abolfazl (Abe) Arab ([@abearab](https://github.com/abearab)) as a Research Associate in the Gilbert lab at UCSF and Arc Institute.
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  ## Citation
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- If you use ScreenPro2 in your research, please cite the following paper.
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+ If you use ScreenPro2 in your research, please cite both the software release and the published paper.
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- Coming soon...
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+ **Final publication note**: The final ScreenPro2 publication is now available in _Nature Chemical Biology_ (2026): https://doi.org/10.1038/s41589-026-02312-z
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+
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+ - **Software (Zenodo)**:
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+ > Arab, A., et al. ArcInstitute/ScreenPro2. _Zenodo_ (2026). https://doi.org/10.5281/zenodo.18884467
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- ## Development
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- ### Testing
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- Tests can be easily run using the `pytest` framework.
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+ - **Paper (Nature Chemical Biology)**:
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+ > O’Loughlin, T.A., Arab, A., et al. **Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response.** _Nat Chem Biol_ (2026). https://doi.org/10.1038/s41589-026-02312-z
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{screenpro2-0.6.1 → screenpro2-0.7.0}/README.md RENAMED
@@ -1,5 +1,6 @@
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  [![website](https://img.shields.io/badge/website-live-brightgreen)](https://arcinstitute.org/tools/screenpro2)
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- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18807934.svg)](https://doi.org/10.5281/zenodo.18807934)
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+ [![zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.18807934.svg)](https://doi.org/10.5281/zenodo.18807934)
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+ [![NCB](https://img.shields.io/badge/DOI-10.1038%2Fs41589--026--02312--z-blue.svg)](https://doi.org/10.1038/s41589-026-02312-z)
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  [![PyPI version](https://badge.fury.io/py/ScreenPro2.svg)](https://badge.fury.io/py/ScreenPro2)
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  [![Documentation Status](https://readthedocs.org/projects/screenpro2/badge/?version=latest)](https://screenpro2.readthedocs.io/en/latest/?version=latest)
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  [![Downloads](https://static.pepy.tech/badge/screenpro2)](https://pepy.tech/project/screenpro2)
@@ -337,10 +338,12 @@ ScreenPro2 is licensed under the terms of the MIT license (see [LICENSE](LICENSE
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  by Abolfazl (Abe) Arab ([@abearab](https://github.com/abearab)) as a Research Associate in the Gilbert lab at UCSF and Arc Institute.
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  ## Citation
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- If you use ScreenPro2 in your research, please cite the following paper.
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+ If you use ScreenPro2 in your research, please cite both the software release and the published paper.
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- Coming soon...
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+ **Final publication note**: The final ScreenPro2 publication is now available in _Nature Chemical Biology_ (2026): https://doi.org/10.1038/s41589-026-02312-z
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+
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+ - **Software (Zenodo)**:
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+ > Arab, A., et al. ArcInstitute/ScreenPro2. _Zenodo_ (2026). https://doi.org/10.5281/zenodo.18884467
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- ## Development
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- ### Testing
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- Tests can be easily run using the `pytest` framework.
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+ - **Paper (Nature Chemical Biology)**:
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+ > O’Loughlin, T.A., Arab, A., et al. **Chemogenomic maps reveal a PRDX1-dependent iron–damage axis in the DNA damage response.** _Nat Chem Biol_ (2026). https://doi.org/10.1038/s41589-026-02312-z
{screenpro2-0.6.1 → screenpro2-0.7.0}/pyproject.toml RENAMED
@@ -1,7 +1,7 @@
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  [tool.poetry]
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  name = "ScreenPro2"
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  description = "Flexible analysis of high-content CRISPR screening"
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- version = "0.6.1"
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+ version = "0.7.0"
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  authors = [
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  "Abolfazl Arab <abolfazl.arab@ucsf.edu>",
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  "Nick Youngblut <nick.youngblut@arcinstitute.org>",
{screenpro2-0.6.1 → screenpro2-0.7.0}/LICENSE RENAMED
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{screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/load.py RENAMED
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{screenpro2-0.6.1 → screenpro2-0.7.0}/screenpro/main.py RENAMED
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