Metadata-Version: 2.4
Name: piaso-tools
Version: 1.0.0
Summary: Precise Integrative Analysis of Single-cell Omics.
Project-URL: Documentation, https://genecell.github.io/PIASO/
Project-URL: Source, https://github.com/genecell/PIASO
Project-URL: Homepage, https://genecell.github.io/PIASO/
Author-email: Min Dai <dai@broadinstitute.org>
Maintainer-email: Min Dai <dai@broadinstitute.org>, Vallari Shende <vshende@broadinstitute.org>
License-Expression: BSD-3-Clause
License-File: LICENSE
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Framework :: Jupyter
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.9
Requires-Dist: anndata>=0.8
Requires-Dist: cosg>=1.0.1
Requires-Dist: matplotlib>=3.5.2
Requires-Dist: numpy>=1.21.6
Requires-Dist: pandas>=1.4.4
Requires-Dist: scanpy>=1.9.1
Requires-Dist: scikit-learn>=1.1
Requires-Dist: scipy>=1.7.3
Requires-Dist: seaborn>=0.11.2
Requires-Dist: statsmodels>=0.13.2
Requires-Dist: tqdm
Requires-Dist: typing-extensions
Provides-Extra: dev
Requires-Dist: pre-commit; extra == 'dev'
Description-Content-Type: text/markdown

# PIASO
### Precise Integrative Analysis of Single-cell Omics

### Documentation

[PIASO documentation](https://genecell.github.io/PIASO/) 

### Current available functionalities

1. perform dimensionality reduction with GDR
2. integration of scRNA-seq datasets with GDR
3. integration of scRNA-seq data and MERFISH/Xenium data with GDR
4. normalization of scRNA-seq data with INFOG
5. selection of highly-variable genes in scRNAseq data with INFOG
6. a novel gene set scoring method
7. run clustering on selected cluster(s)
8. side-by-side cell embedding plots, e.g., split by Conditions
9. stacked violin plots for multiple features, including genes and cell metrics

### Coming functionalities

1. preprocessing of scATAC-seq datasets
2. integration of scRNA-seq and scATAC-seq datasets (not relying on gene activities)
3. inference of cell type-specific gene regulatory networks
4. and others

### Citation

If PIASO is useful for your research, please consider citing [Wu et al., Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypes, bioRxiv (2024)](https://www.biorxiv.org/content/10.1101/2024.07.20.604399v1). 

### Contact
Min Dai
dai@broadinstitute.org