https://github.com/mvinyard/archr-h5ad

Parse ArchR arrow files to anndata h5ad
https://github.com/mvinyard/archr-h5ad

io r-to-python scatac-seq single-cell

Last synced: 4 months ago
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Parse ArchR arrow files to anndata h5ad

• Host: GitHub
• URL: https://github.com/mvinyard/archr-h5ad
• Owner: mvinyard
• License: mit
• Created: 2022-05-17T19:35:31.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2023-12-14T14:42:37.000Z (almost 2 years ago)
• Last Synced: 2025-06-01T20:52:33.856Z (4 months ago)
• Topics: io, r-to-python, scatac-seq, single-cell
• Language: Python
• Homepage:
• Size: 29.3 KB
• Stars: 12
• Watchers: 1
• Forks: 3
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# ArchR-h5ad

[![PyPI pyversions](https://img.shields.io/pypi/pyversions/ArchR-h5ad.svg)](https://pypi.python.org/pypi/ArchR-h5ad/)

[![PyPI version](https://badge.fury.io/py/ArchR-h5ad.svg)](https://badge.fury.io/py/ArchR-h5ad)

[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)

A lightweight python package to parse **[`.arrow`]()** files produced by [**ArchR**](https://www.archrproject.com) - to [**AnnData**](https://anndata.readthedocs.io/en/stable/).

## Installation

Install the last-released ([**`v0.0.12`**](https://pypi.org/project/ArchR-h5ad/0.0.12/)) distrubution from [PYPI](https://pypi.org/project/ArchR-h5ad/):

```BASH

pip install ArchR_h5ad

```

Alternatively, clone the repo to install the development version, locally:

```BASH

git clone https://github.com/mvinyard/ArchR-h5ad.git; cd ArchR_h5ad

pip install -e .

```

## A brief example

As an example, we will use the data from the ArchR [hematopoiesis tutorial](https://www.archrproject.com/articles/Articles/tutorial.html#creating-an-archrproject-1).

### Option 1. Directly read a `.arrow` file to adata

```python

import ArchR_h5ad

arrow_path = "/home/user/data/scATAC_CD34_BMMC_R1.arrow"

adata = ArchR_h5ad.read_arrow(arrow_path, use_matrix="GeneScoreMatrix")

```



Alternatively, one may use the **`"TileMatrix"`** generated by ArchR. 

```python

adata = ArchR_h5ad.read_arrow(arrow_path, use_matrix="TileMatrix")

```



### Option 2. Instantiate the `Arrow` class.

```python

arrow = ArchR_h5ad.Arrow(arrow_path)

arrow.to_adata()

```



```python

import numpy as np

np.array(arrow.__dir__())[

    np.array([not i.startswith("__") for i in arrow.__dir__()])

].tolist()

```