For a full list of our lab’s open-source bioinformatics 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 Software / Hobby Projects