Single-cell RNA-seq analysis for transcriptomic type characterization
This is the umbrella package for the
scrattch suite of R packages from the Allen Institute for Brain Science. It is modeled after the
You can use
scrattch to automatically install or update these packages:
scrattch.io - File handling and data formatting
scrattch.hicat - Hierarchical, iterative clustering for analysis of transcriptomics
scrattch.bigcat - Clustering analysis for extremely large single cell dataset
scrattch.vis - Plotting functions for visualization of RNA-seq data
tasic2016data - Data from Tasic, et al. (2016), which is used for demos
If you're interested in only one of these modules, you can install them separately.
scrattch will install them all together.
To install all scrattch packages along with their Github and BioConductor dependencies, use:
Should you need the previous version, it can still be installed using:
devtools::install_github("AllenInstitute/scrattch", ref = "archive")
There are now a lot of functions available in
scrattch packages. To assist in finding what package a function is stored in, you can check this CSV file stored in the
scrattch umbrella package:
scrattch function list
The license for this package is available on Github at: https://github.com/AllenInstitute/scrattch/blob/master/LICENSE
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/blob/master/CONTRIBUTION
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.