Repositories list

• STcompare

  Public
  STcompare is an R package for comparing spatial gene expression patterns across spatial transcriptomics (ST) datasets

  statisticsrstatsspatial-analysis+ 3

  statisticsrstatsspatial-analysisdifferential-expressionspatial-transcriptomicsspatial-omics

  R

  •0•7•2•0•Updated Mar 20, 2026Mar 20, 2026

• CellCarto-ColdIschemia

  Public
  CSS

  •0•0•0•0•Updated Mar 20, 2026Mar 20, 2026

• genomic-data-visualization-2026

  Public
  JavaScript

  •28•0•0•5•Updated Mar 14, 2026Mar 14, 2026

• off-target-probe-tracker

  Public
  Pipeline to predict off-target binding via probe sequences

  Python

  •

  GNU General Public License v3.0

  •2•14•0•0•Updated Mar 13, 2026Mar 13, 2026

• Mentorship-Index

  Public

  JEFworks-Lab/Mentorship-Index’s past year of commit activity
  A website for calculating a scientist's Mentorship Index (M-index), which measures a their contribution to mentoring early-career scientists.

  HTML

  •0•1•0•0•Updated Mar 2, 2026Mar 2, 2026

• jefworks-lab.github.io

  Public
  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •30•4•1•1•Updated Mar 1, 2026Mar 1, 2026

• CellCarto-3DEEP

  Public

  JEFworks-Lab/CellCarto-3DEEP’s past year of commit activity
  3DEEP Hair Follicle Data Explorer

  JavaScript

  •1•0•0•0•Updated Feb 25, 2026Feb 25, 2026

• GestureGraph

  Public
  Gesture-based Interactive Exploration of Single Cell Embeddings

  JavaScript

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Jan 13, 2026Jan 13, 2026

• CellCarto-OvulationSlideseq

  Public
  Cellular Cartography Spatial Transcriptomics Data Explorer for a Time-course of ovulating mouse ovaries assayed by Slide-seq

  JavaScript

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Jan 5, 2026Jan 5, 2026

• CellCarto-MouseEmbryoMERFISH

  Public
  Cellular Cartography Spatial Transcriptomics Data Explorer for an E15.5 mouse embryo assayed by MERFISH

  JavaScript

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Dec 30, 2025Dec 30, 2025

• SVG-Text-Standardizer

  Public
  standardize text sizes, fonts, and remove stretching for publication-quality figures

  JavaScript

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Dec 29, 2025Dec 29, 2025

• STARIT

  Public
  Spatial Transcriptomics As Rasterized Tensors (STARIT)

  bioinformaticsspatial-analysisrasterization+ 2

  bioinformaticsspatial-analysisrasterizationspatial-transcriptomicsspatial-omics

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Dec 10, 2025Dec 10, 2025

• CRAWDAD

  Public
  Cell-type Relationship Analysis Workflow Done Across Distances

  proteomicsspatial-analysistranscriptomics+ 1

  proteomicsspatial-analysistranscriptomicsspatial-omics

  R

  •

  GNU General Public License v3.0

  •7•42•4•0•Updated Nov 18, 2025Nov 18, 2025

• STdeconvolve

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

  R

  •19•154•21•0•Updated Aug 3, 2025Aug 3, 2025

• SEraster

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

  rstatsspatial-analysisspatial-data-analysis+ 2

  rstatsspatial-analysisspatial-data-analysisspatial-transcriptomicsspatial-omics

  R

  •5•19•2•0•Updated Apr 23, 2025Apr 23, 2025

• genomic-data-visualization-2025

  Public
  JavaScript

  •29•0•0•0•Updated Mar 14, 2025Mar 14, 2025

• scatterbar

  Public
  Scatterbar - data visualization for proportional data across many spatially resolved coordinates

  data-visualizationspatial-analysisspatial-data-analysis+ 1

  data-visualizationspatial-analysisspatial-data-analysisspatial-transcriptomics

  R

  •

  GNU General Public License v3.0

  •1•11•1•0•Updated Mar 3, 2025Mar 3, 2025

• HuBMAP_Workspaces_WIP

  Public
  Work-in-progress templates for HuBMAP workspaces

  Jupyter Notebook

  •3•0•0•0•Updated Nov 4, 2024Nov 4, 2024

• genomic-data-visualization-2024

  Public
  Course website for Genomic Data Visualization 2024

  JavaScript

  •36•26•0•1•Updated Mar 15, 2024Mar 15, 2024

• STalign

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

  bioinformaticsalignmentdiffeomorphism+ 2

  bioinformaticsalignmentdiffeomorphismsinglecellspatialtranscriptomics

  HTML

  •

  GNU General Public License v3.0

  •24•95•21•2•Updated Dec 11, 2023Dec 11, 2023

• genomic-data-visualization-2023

  Public
  Course website for Genomic Data Visualization 2023

  JavaScript

  •20•10•0•0•Updated Mar 11, 2023Mar 11, 2023

• MERmaid

  Public
  WebGL-based viewer for spatially-resolved transcriptomics data

  javascriptwebglreactjs+ 3

  javascriptwebglreactjsdata-visualizationsingle-cellspatial-transcriptomics

  JavaScript

  •5•28•4•18•Updated Jan 6, 2023Jan 6, 2023

• genomic-data-visualization-2022

  Public
  Course website for Genomic Data Visualization 2022

  JavaScript

  •18•16•1•0•Updated Dec 28, 2022Dec 28, 2022

• veloviz

  Public
  RNA-velocity informed embeddings for visualizing cellular trajectories

  R

  •

  GNU General Public License v3.0

  •3•45•1•0•Updated Sep 5, 2022Sep 5, 2022

• MERINGUE

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

  gene-expressionrstatsspatial-analysis+ 3

  gene-expressionrstatsspatial-analysissingle-cellspatial-transcriptomicscell-cell-communication

  R

  •

  GNU General Public License v3.0

  •7•90•7•0•Updated Jun 7, 2022Jun 7, 2022

• snakepit

  Public
  snakemake files

  0•0•0•0•Updated May 6, 2022May 6, 2022

• HoneyBADGER

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

  hmmbioinformaticsbayesian+ 6

  hmmbioinformaticsbayesiantranscriptomicssubpopulationheterogeneitysingle-cell-rna-seqsingle-cell-analysiscnv-detection

  R

  •

  GNU General Public License v3.0

  •30•102•14•1•Updated Jul 19, 2021Jul 19, 2021

• NSF_CAREER

  Public
  0•0•0•0•Updated Apr 15, 2021Apr 15, 2021

• R-style-guide

  Public
  Best practices for readable, sharable, and verifiable R code

  styleguidebest-practicescollaboration+ 1

  styleguidebest-practicescollaborationrstats

  HTML

  •

  MIT License

  •1•18•0•0•Updated Mar 26, 2019Mar 26, 2019