swh:1:snp:0da231f3ffdb3226650880f1b61d5d5cdcbd749b
Tip revision: 49a1be0427f2f26a531eb468ba93eeb18d8a2edb authored by satijalab on 13 December 2019, 20:42:25 UTC
Merge pull request #2416 from satijalab/develop
Merge pull request #2416 from satijalab/develop
Tip revision: 49a1be0
README.md
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# Seurat v3.1.2
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:
* https://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
August 20, 2019
* Version 3.1
* Changes:
* Support for SCTransform integration workflows
* Integration speed ups: reference-based integration + reciprocal PCA
April 12, 2019
* Version 3.0
* Changes:
* Preprint published describing new methods for identifying anchors across single-cell datasets
* Restructured Seurat object with native support for multimodal data
* Parallelization support via future
July 20, 2018
* Version 2.4
* Changes:
* Java dependency removed and functionality rewritten in Rcpp
March 22, 2018
* Version 2.3
* Changes:
* New utility functions
* Speed and efficiency improvments
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)