readseurat
Read Seurat .rds and .h5seurat files into AnnData — implemented in pure Python, no R required.
The code for rds parsing is based on the rdata package (https://github.com/vnmabus/rdata).
Installation
pip install readseurat
Python API
import readseurat
# Read an RDS file containing a Seurat object
adata = readseurat.read_seurat("pbmc3k.rds")
# Read an H5Seurat file
adata = readseurat.read_h5seurat("pbmc3k.h5seurat")
Commandline
Convert a Seurat file to H5AD format:
# From RDS
readseurat convert pbmc3k.rds pbmc3k.h5ad
# From H5Seurat
readseurat convert pbmc3k.h5seurat pbmc3k.h5ad
Usage: readseurat convert [OPTIONS] INPUT OUTPUT
Convert a Seurat file (RDS or H5Seurat) to H5AD format.
Options:
--format [rds|h5seurat] Input file format. Inferred from file extension if
not specified.
-h, --help Show this message and exit.
Citation
rdata package:
Ramos-Carreño, C., & Rossi, T. (2024). rdata: A Python library for R datasets. Journal of Open Source Software, 9(104), 1–4. https://doi.org/10.21105/joss.07540
1 maintainer
Metadata
1 maintainer
Release files for readseurat 0.1.0
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Source distribution (sdist)
| File | Size | Uploaded | |
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| readseurat-0.1.0.tar.gz | 36.3 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| readseurat-0.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 81.2 kB
Release files / readseurat-0.1.0.tar.gz
| Download URL | readseurat-0.1.0.tar.gz |
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| Size | 36.3 kB |
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Release files / readseurat-0.1.0-py3-none-any.whl
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| Size | 44.9 kB |
| Tags | Python 3 |
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uv/0.10.10 {"installer":{"name":"uv","version":"0.10.10","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
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