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JEFworks Lab's Projects

crawdad icon crawdad

Cell-type Relationship Analysis Workflow Done Across Distances

honeybadger icon honeybadger

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

meringue icon meringue

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

mermaid icon mermaid

WebGL-based viewer for spatially-resolved transcriptomics data

r-style-guide icon r-style-guide

Best practices for readable, sharable, and verifiable R code

seraster icon seraster

Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis

stalign icon stalign

Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping

stdeconvolve icon stdeconvolve

Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data

veloviz icon veloviz

RNA-velocity informed embeddings for visualizing cellular trajectories

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