scrattch.hicat: Hierarchical, Iterative Clustering for Analysis of Transcriptomics
Installation
scrattch.hicat has several dependencies, including two from BioConductor and one from Github:
source("https://bioconductor.org/biocLite.R")
biocLite("limma")
devtools::install_github("JinmiaoChenLab/Rphenograph")
Once these dependencies are installed, scrattch.hicat can be installed with:
devtools::install_github("AllenInstitute/scrattch.hicat")
Vignettes
An overview of the main functions in scrattch.hicat
Tutorials
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.
License
The license for this package is available on Github at: https://github.com/AllenInstitute/scrattch.hicat/blob/master/LICENSE
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: https://github.com/AllenInstitute/scrattch.hicat/blob/master/CONTRIBUTION
Image attribution:
By Internet Archive Book Images [No restrictions], via Wikimedia Commons