Tutorial • nicheDE

Niche-DE Tutorial

This page contains tutorials for using the nicheDE package in R. Each step in the niche-DE process is described in detail; from the initial deconvolution step to downstream processes such as niche ligand-receptor analysis. Click the links below to visit a specific step in the pipeline.

Installing Niche-DE

Installation: How to download Niche-DE using devtools.

Deconvolution

Deconvolution: A step by step guide for performing cell type deconvolution of your spatial transcriptomic data using RCTD.
Average Expression Profile: A guide on how to calculate the average expression profile matrix from your reference dataset.

Creating Your Niche-DE Object

Object Creation: A guide on how to create your own niche-DE object starting from a spatial seurat object or raw data matrices.
Effective Niche Calculation: A guide on how to calculate the effective niche as well as suggested guidelines on how to choose the kernel bandwidth.
Merging and Filtering: A guide on how to merge multiple niche-DE objects or filter out observations from a niche-DE object.

Performing Niche-DE

Performing Niche-DE: A guide on how to run niche-DE once you have your niche-DE object.

Downstream Analysis

Getting Niche-DE Genes: A guide on how to get niche-DE genes between a given index and niche cell type as well as how to perform pathway enrichment analysis given these niche-DE genes.
Marker Genes: A guide on performing marker gene analysis using niche-DE
Ligand Receptor Analysis: A guide on performing ligand-receptor analysis using niche-DE.