Harmonic analysis of spatial transcriptomics data

⬅️ manuscript

This repository includes

1. a minimal package for performing filtering
2. all notebooks used to generate figures

See instructions below for installing and using the package.

1. Installation

pip install git+https://github.com/wanglab-broad/harmonics@main

2. Usage

This package can be used in Python as follows:

import scanpy as sc
import harmonics as hm

# Load data
adata = sc.read_h5ad('/path/to/your/data.h5ad')

# High-pass filter genes using a square-root (i.e. juxtacrine interaction) kernel
hm.sfilter(
    adata,
    'juxtacrine',
)

For a list of parameters, their meanings, and their types, run help(hm.sfilter).

Alternatively, one can run hm.sfilter from the shell:

harmonics \
--read_path /path/to/your/data.h5ad \
--write_path /path/to/your/filtered_data.h5ad \
--filter_keys juxtacrine \

For a list of parameters in the shell, run harmonics --help.