{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Tutorial 4: Peak selection analysis" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Here we will use scATAC-seq dataset `10XBlood' as an example to train scAGDE and analyse the peak importance scores model have learned." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 1. Train scAGDE" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "First we train scAGDE on the 10XBlood dataset following [Tutorial 1: End-to-end scATAC-seq analysis](./Tutorial%201:%20End-to-end%20scATAC-seq%20analysis.ipynb)." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "import scanpy as sc\n", "adata = sc.read_h5ad(\"data/10XBlood.h5ad\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "