Metadata-Version: 2.4
Name: monocle2-python
Version: 2.9.0
Summary: Python port of the R monocle2 package (tracks cole-trapnell-lab/monocle-release 2.9.0 @ 7df1050) — single-cell trajectory, differential expression, BEAM.
Project-URL: Homepage, https://github.com/Bio-Babel/Monocle2-python
Project-URL: Repository, https://github.com/Bio-Babel/Monocle2-python
Project-URL: Issues, https://github.com/Bio-Babel/Monocle2-python/issues
Project-URL: Documentation, https://github.com/Bio-Babel/Monocle2-python#readme
Project-URL: Upstream (R package), https://github.com/cole-trapnell-lab/monocle-release
Project-URL: Tutorial data (Zenodo), https://zenodo.org/records/19699224
Author-email: Jeffery Liu <jeffliu.lucky@gmail.com>
License-Expression: Artistic-2.0
License-File: LICENSE
Keywords: BEAM,DDRTree,R-port,differential-expression,monocle,monocle2,pseudotime,scRNA-seq,single-cell,trajectory
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Typing :: Typed
Requires-Python: >=3.10
Requires-Dist: anndata>=0.10
Requires-Dist: ddrtree-python>=0.1.6
Requires-Dist: ggplot2-python>=4.0.2.9000
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Requires-Dist: pandas>=2.0
Requires-Dist: patsy>=0.5
Requires-Dist: pheatmap-python>=1.0.13
Requires-Dist: python-igraph>=0.10
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Requires-Dist: scales-python>=1.4.0
Requires-Dist: scikit-learn>=1.3
Requires-Dist: scipy>=1.10
Requires-Dist: statsmodels>=0.14
Provides-Extra: dev
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Requires-Dist: mkdocstrings[python]; extra == 'docs'
Description-Content-Type: text/markdown

# monocle2-python

[![PyPI](https://img.shields.io/pypi/v/monocle2-python)](https://pypi.org/project/monocle2-python/)

Python port of the R [**monocle2**](https://github.com/cole-trapnell-lab/monocle-release) single-cell trajectory toolkit.

## Installation

```bash
pip install monocle2-python                # from PyPI
```

For local development:

```bash
git clone https://github.com/Bio-Babel/Monocle2-python.git
cd Monocle2-python
pip install -e ".[dev]"
```


## Quickstart

```python
import monocle2py as m2

cds = m2.load_hsmm_fpkm()
m2.estimate_size_factors(cds)
m2.estimate_dispersions(cds)
m2.reduce_dimension(cds, reduction_method="DDRTree")
m2.order_cells(cds)
m2.plot_cell_trajectory(cds, color_by="State")
```

## Tutorials

Four runnable notebooks that reproduce the R monocle2 tutorials live under [`tutorials/`](tutorials/):

| Notebook | Dataset |
|---|---|
| `V2_1_HSMM.ipynb` | HSMM myoblast differentiation |
| `V2_2_lung_BEAM.ipynb` | Lung epithelium BEAM walkthrough |
| `V2_3_Olsson_corrected.ipynb` | Olsson myeloid progenitors (WT + KOs) |
| `V2_4_Paul.ipynb` | Paul hematopoiesis |

## License

Artistic-2.0, matching the upstream R monocle2.
