Tools for pre-processing and visualizing Visium HD spatial transcriptomics data.
Features
Read in raw VisiumHD data and convert to SpatialData objects
Quality control metric plotting and image plotting
Destripe counts from raw 2um bins
Write updated counts back to raw VisiumHD data format
Installation
Install from PyPI:
pip install visiumhd-utilsUsage
import visiumhd_utils.read_data as rd
import visiumhd_utils.qc_plot as qp
import visiumhd_utils.destripe as ds
import visiumhd_utils.write_data as wd
sdata = rd.to_spatialdata("path/to/data", "id")
qp.compute_qc_metrics(sdata)
qp.plot_qc_metrics(sdata, "id", metric="pct_counts_mt")
ds.destripe_b2c(sdata)
wd.write_2um_filtered_counts(sdata, "path/to/folder")Project Status
This package is in early development. Use with caution; interfaces may change.
Note
This project has been set up using PyScaffold 4.6. For details and usage information on PyScaffold see https://pyscaffold.org/.
1 maintainer
Release files for visiumhd-utils 0.2.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| visiumhd_utils-0.2.2.tar.gz | 26.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| visiumhd_utils-0.2.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 36.8 kB
Release files / visiumhd_utils-0.2.2.tar.gz
| Download URL | visiumhd_utils-0.2.2.tar.gz |
|---|---|
| Size | 26.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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Release files / visiumhd_utils-0.2.2-py3-none-any.whl
| Download URL | visiumhd_utils-0.2.2-py3-none-any.whl |
|---|---|
| Size | 10.0 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
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twine/6.1.0 CPython/3.9.14
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