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scrattch

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 tidyverse package.

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.

Installation

To install all scrattch packages along with their Github and BioConductor dependencies, use:

devtools::install_github("AllenInstitute/scrattch")

scrattch::install_scrattch()

The previous, internal version of scrattch has been split to two packages:
File handling and data formatting are now part of scrattch.io.
Plotting and visualization are now part of scrattch.vis.

Should you need the previous version, it can still be installed using:

devtools::install_github("AllenInstitute/scrattch", ref = "archive")

Function List

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

License

The license for this package is available on Github at: https://github.com/AllenInstitute/scrattch/blob/master/LICENSE

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/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.

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