A Julia package for single cell and spatial data analysis
MERlin is an extensible analysis pipeline applied to decoding MERFISH data
A package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and statistically enriched covariation of gene programs between interacting cell types from the neighborhood.
GPU accelerated post-processing for 2D or 3D imaging spatial transcriptomics data.
A python toolkit for spatial domains and spatially variable genes discovery for high-resolution spatially resolved transcriptomics data.
Single cell ATAC and RNA seq data analysis
Bioinformatics data pipelines and workflows developed and implemented to support genomics studies at the Center for Brain Immunology and Glia (BIG), University of Virginia.
First step of data wrangling in MERFISH data project
Spatial transcriptomics analysis pipeline — BANKSY, scVI, Tangram, COMMOT, Augur
Pre-processing script for Vizgen MERFISH data
A wrapper for the CellNeighborEX python library (all credits go to Hyobin Kim) made as part of a greater project for analyzing MERFISH spatial transcriptomics data
Performs barcode-decoding quality control for FISH-based spatial transcriptomic runs
A snakemake pipeline to perform cell segmentation on MERFISH spatial transcriptomics data.
BioWorkbench
Efficiently parse transcripts metadata from the detected_transcripts.csv file generated by Vizgen MERFISH pipeline.
🥈 2nd place · UR Biomedical Data Science Hackathon 2026 — MERFISH spatial-transcriptomics cell-type classification (60 classes). Biology-constrained 5-model ensemble, leave-one-mouse-out validation, EDA + data dictionary, and a post-competition study showing accuracy scales 0.77.
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