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Software
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software

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

BIOINFORMATICS SOFTWARE

  • scatterbar - R package for visualizing proportional data across many spatially resolved coordinates

  • SEraster - R package for rasterization preprocessing of spatial omics data

  • CRAWDAD - R package for characterizing cell-type spatial relationships across length scales

  • 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

FUN STUFF