ArchR_h5ad: Read .arrow files (from ArchR) to anndata.
Project description
ArchR-h5ad
A lightweight python package to parse .arrow
files produced by ArchR - to AnnData.
Installation
Install the last-released (v0.0.1
) distrubution from PYPI:
pip install ArchR_h5ad
Alternatively, clone the repo to install the development version, locally:
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.
Option 1. Directly read a .arrow
file to adata
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.
adata = ArchR_h5ad.read_arrow(arrow_path, use_matrix="TileMatrix")
Option 2. Instantiate the Arrow
class.
arrow = ArchR_h5ad.Arrow(arrow_path)
arrow.to_adata()
import numpy as np
np.array(arrow.__dir__())[
np.array([not i.startswith("__") for i in arrow.__dir__()])
].tolist()
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