NICHES

NICHES is a central software backbone for many projects in our lab. It is computationally efficient, highly adaptable, and statistically powerful.

NICHESMethods

Raredon Lab functions and scripts for public and collaborator use. Constantly developing.

Formalizes and builds on methods from Greaney & Raredon et al 2024.

Connectome

This is a first-generation package to analyze cell-cell signaling information in tissues. It is accurate, fast, and simple.

Teaching Vignettes

This is a collection of vignettes showing standardized ways of processing data for NICHES analysis.

Dissociation Guides

Public protocols for dissociation of lung tissues.

Pulmonary Bioengineering

Public protocols for engineering lung tissues.

Organoid Engineering

Public protocols for pulmonary organoids.

Cross-Species Pulmonary Atlas

Data from Raredon et al. 2019.

Microvascular Fluid Flow Data from Native and Engineered Lung

Data from Raredon et al. 2021.

A ggplot2 Tutorial for Beautiful Plotting in R

By Cedric Scherer

Seurat

By Satija Lab

ComplexHeatmap

By Jokergoo

Best practices for single-cell data analysis

By Leucken & Theis

IPF Cell atlas

By Kaminski Lab