For a full list of our software, please see our Github page


  • STalign - Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  • STdeconvolve - R package for reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  • MERINGUE - R package for characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with non-uniform cellular densities
  • VeloViz - R package for creating RNA-velocity-informed 2D embeddings for single cell transcriptomics data
  • MERmaid - WebGL-based viewer for MERFISH data

  • HoneyBADGER - R package for detecting copy number alteration at the single cell level from single cell RNA-seq data
  • SCDE/PAGODA - R package for single cell differential expression and pathway and gene set over-dispersion analysis
  • brainmapr - R package to infer spatial location of neuronal subpopulations within the developing mouse brain by integrating single cell RNA-seq data with in situ hybridization data from the Allen Developing Mouse Brain Atlas
  • LIGER - a light-weight R implementation of the Broad Gene Set Enrichment Analysis algorithm
  • UBIT2 - user-friendly bioinformatics webtool for analyzing single cell transcriptomic data