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Seurat v2.2

Seurat is an R toolkit for single cell genomics, developed and maintained by the Satija Lab at NYGC.

Instructions, documentation, and tutorials can be found at: * http://www.satijalab.org/seurat

Seurat is also hosted on GitHub, you can view and clone the repository at * https://github.com/satijalab/seurat

Seurat has been successfully installed on Mac OS X, Linux, and Windows, using the devtools package to install directly from GitHub

Improvements and new features will be added on a regular basis, please contact seuratpackage@gmail.com with any questions or if you would like to contribute

Version History

January 10, 2018 * Version 2.2 * Changes: * Support for multiple-dataset alignment with RunMultiCCA and AlignSubspace * New methods for evaluating alignment performance

October 12, 2017 * Version 2.1 * Changes: * Support for using MAST and DESeq2 packages for differential expression testing in FindMarkers * Support for multi-modal single-cell data via @assay slot

July 26, 2017 * Version 2.0 * Changes: * Preprint released for integrated analysis of scRNA-seq across conditions, technologies and species * Significant restructuring of code to support clarity and dataset exploration * Methods for scoring gene expression and cell-cycle phase

October 4, 2016 * Version 1.4 released * Changes: * Improved tools for cluster evaluation/visualizations * Methods for combining and adding to datasets

August 22, 2016: * Version 1.3 released * Changes : * Improved clustering approach - see FAQ for details * All functions support sparse matrices * Methods for removing unwanted sources of variation * Consistent function names * Updated visualizations

May 21, 2015: * Drop-Seq manuscript published. Version 1.2 released * Changes : * Added support for spectral t-SNE and density clustering * New visualizations - including pcHeatmap, dot.plot, and feature.plot * Expanded package documentation, reduced import package burden * Seurat code is now hosted on GitHub, enables easy install through devtools * Small bug fixes

April 13, 2015: * Spatial mapping manuscript published. Version 1.1 released (initial release)