/seurat

R toolkit for single cell genomics

Primary LanguageRGNU General Public License v3.0GPL-3.0

About this Repository

This is a fork of the now outdated Seurat v4.0 Beta repository modified for our own version of multi-way WNN analysis in Swanson, et al., eLife, 2021 prior to the availability of multi-way WNN in the Seurat v4.0 Beta.

Multi-way WNN analysis is now implemented in the Release version of Seurat v4.0 using the FindMultimodalNeighbors() function.

We recommend that users utilize the official implementation rather than this repository unless reproducing analysis from Swanson, et al.

Build Status AppVeyor build status CRAN Version CRAN Downloads

Seurat v4.0 Beta

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:

Seurat is also hosted on GitHub, you can view and clone the repository at

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

July 15, 2020

  • Version 3.2
  • Changes:
    • Support for analysis and visualization of spatially resolved datasets

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)