JEFworks Lab

All

17 repositories

STdeconvolve
Public
Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
R
•12•104•18•0•Updated Nov 5, 2024Nov 5, 2024
jefworks-lab.github.io
Public
Jupyter Notebook
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Creative Commons Attribution 4.0 International
•27•4•1•0•Updated Nov 4, 2024Nov 4, 2024
HuBMAP_Workspaces_WIP
Public
Work-in-progress templates for HuBMAP workspaces
Jupyter Notebook
•3•0•0•0•Updated Nov 4, 2024Nov 4, 2024
CRAWDAD
Public
Cell-type Relationship Analysis Workflow Done Across Distances
proteomics spatial-analysis transcriptomics spatial-omics
R
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GNU General Public License v3.0
•3•22•1•0•Updated Nov 1, 2024Nov 1, 2024
scatterbar
Public
Scatterbar - data visualization for proportional data across many spatially resolved coordinates
data-visualization spatial-analysis spatial-data-analysis spatial-transcriptomics
R
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GNU General Public License v3.0
•0•2•1•0•Updated Oct 18, 2024Oct 18, 2024
SEraster
Public
Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis
rstats spatial-analysis spatial-data-analysis spatial-transcriptomics spatial-omics
R
•4•16•1•0•Updated Sep 24, 2024Sep 24, 2024
genomic-data-visualization-2024
Public
Course website for Genomic Data Visualization 2024
JavaScript
•32•22•0•0•Updated Mar 15, 2024Mar 15, 2024
STalign
Public
Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
bioinformatics alignment diffeomorphism singlecell spatialtranscriptomics
HTML
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GNU General Public License v3.0
•13•67•7•1•Updated Dec 11, 2023Dec 11, 2023
genomic-data-visualization-2023
Public
Course website for Genomic Data Visualization 2023
JavaScript
•19•9•0•0•Updated Mar 11, 2023Mar 11, 2023
MERmaid
Public
WebGL-based viewer for spatially-resolved transcriptomics data
javascript webgl reactjs data-visualization single-cell spatial-transcriptomics
JavaScript
•5•26•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
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GNU General Public License v3.0
•3•43•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-expression rstats spatial-analysis single-cell spatial-transcriptomics cell-cell-communication
R
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GNU General Public License v3.0
•5•58•6•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
hmm bioinformatics bayesian transcriptomics subpopulation heterogeneity single-cell-rna-seq single-cell-analysis cnv-detection
R
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GNU General Public License v3.0
•31•96•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
styleguide rstats best-practices collaboration
HTML
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MIT License
•1•17•0•0•Updated Mar 26, 2019Mar 26, 2019