scrattch.hicat: Hierarchical, Iterative Clustering for Analysis of Transcriptomics

A hicat


scrattch.hicat has several dependencies, including two from BioConductor and one from Github:



Once these dependencies are installed, scrattch.hicat can be installed with:



An overview of the main functions in scrattch.hicat


An interactive walkthrough of the major steps in clustering for scrattch.hicat.

The scrattch suite

scrattch.hicat is one component of the scrattch suite of packages for Single Cell RNA-seq Analysis for Transcriptomic Type CHaracterization from the Allen Institute.


The license for this package is available on Github at:

Level of Support

We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests.

Contribution Agreement

If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in full at:

Image attribution:

By Internet Archive Book Images [No restrictions], via Wikimedia Commons

AllenInstitute/scrattch.hicat documentation built on Feb. 26, 2019, 6:38 p.m.