visiumhd_utils

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-utils

Usage

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/.