Getting Started

Installation

It is recommended to install the package in a virtual environment or a Conda environment. To create a Conda environment, run the following command:

conda create -n easydecon python=3.10.14
conda activate easydecon

You can install from PyPi:

pip install easydecon

To install directly from GitHub using pip into the active environment, run the following command:

pip install git+https://github.com/sinanugur/easydecon.git

Absolute Minimal Usage

from easydecon.easydecon import *
from easydecon.config import *
from easydecon.extra import *

# read your DESeq table into a markers_df
# sdata is your VisiumHD file in SpatialData format or segmented AnnData object,
# assumed you QC and etc.
markers_df = read_markers_dataframe(sdata, filename="scanpy_deseq_table.csv")

# run easydecon
ph1, ph2, assigned_labels, posterior_df, proportions_df = easydecon_workflow(
    sdata, markers_df=markers_df
)

# or setting prior genes
ph1, ph2, assigned_labels, posterior_df, proportions_df = easydecon_workflow(
    sdata,
    markers_df=markers_df,
    marker_genes=["gene1", "gene2", "gene3"],
)