Community Tools

This page lists helpful tools developed by RBK projects as well as the kidney research community.

Atlas of healthy and injured cell states and niches in the human kidney

Single-cell and single-nucleus assays were applied to a broad spectrum of healthy reference and disease kidneys. This has provided a high-resolution cellular atlas that includes rare and novel cell populations. Based on data generated by teams in the Human BioMolecular Atlas Program (HuBMAP) and Kidney Precision Medicine Project (KPMP) consortia in collaboration with the Human Cell Atlas (CZI) CellxGene to display the datasets.

Azimuth :: Human Kidney Reference

Human BioMolecular Atlas Program (HuBMAP)'s Azimuth is a web app for reference-based single-cell analysis. Upload a counts matrix from a single-cell or single-nucleus RNA-seq dataset of human kidney or load the demo dataset for testing.

Kidney Cell Explorer

A shiny app to explore an adult mouse kidney single cell dataset organized with schematics of epithelial cell structures. Includes subsets of the nephrogenic and ureteric epithelial lineages. From the McMahon Lab (USC Stem Cell, University of Southern California).

Kidney Interactive Transcriptomics

Searchable web tool that allows users to query gene expression across several single cell datasets from human kidney samples. From the Humphreys Lab (Washington University in St. Louis).

Kidney-Omics Databases

Links to transcriptomic and proteomic databases for the various renal tubule epithelia compiled from published papers. From Mark Knepper (Epithelial Systems Biology Laboratory, NHLBI).

Kidney Tissue Atlas Explorer

Search by marker gene, cell type, or data type to view summary data visualizations across the various Kidney Precision Medicine Project (KPMP) 'omics' technologies.

PIVOT

Platform for Interactive analysis and Visualization Of Transcriptomics data, PIVOT facilitates fast and interactive RNA-Seq data analysis and visualization on a Shiny framework. From the Kim Lab (University of Pennsylvania).