RNA-seq Tools

Jointly defining cell types from multiple single-cell datasets using LIGER. LIGER (Linked Inference of Genomic Experimental Relationships). LIGER (liger) is a package for integrating and analyzing multiple single-cell datasets, developed by the Macosko lab and maintained/extended by the Welch lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors.

Ultrafast universal RNA-seq data aligner.

Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.