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    35 repositories

    • whisper

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 1, 2025Nov 1, 2025

    • rakaia

      Public
      🎇 Scale interactive spatial omics in the browser to thousands of images | https://rakaia.io/
      browserviewerspatial-analysisspatial-dataomicsspatial-proteomicsspatial-transcriptomicsmultiplexed-imagingimaging-mass-cytometryspatial-biology
      Python
      •
      Other
      •1•11•4•1•Updated Oct 31, 2025Oct 31, 2025

    • genbait

      Public
      GENBAIT: Genetic Algorithm for Bait Selection
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 27, 2025Oct 27, 2025

    • hmiVAE_manuscript

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 8, 2025Sep 8, 2025

    • hmiVAE

      Public
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Sep 8, 2025Sep 8, 2025

    • genbait_reproducibility

      Public
      GENBAIT Reproducibility
      Python
      •0•0•0•0•Updated Jul 29, 2025Jul 29, 2025

    • astir

      Public
      astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
      machine-learningmultiplexed-imagingimaging-mass-cytometry
      Python
      •
      GNU General Public License v2.0
      •13•57•6•9•Updated Jun 25, 2025Jun 25, 2025

    • twocan

      Public
      A Bayesian optimization framework for multimodal registration of highly multiplexed single-cell spatial proteomics data
      Jupyter Notebook
      •
      Other
      •0•2•0•0•Updated Jun 23, 2025Jun 23, 2025

    • PDAC_cellular_niche_analyses

      Public
      Code implementing the analysis workflow and the probabilistic model for decoding multicellular ecosystems in PDAC
      R
      •0•3•0•0•Updated May 23, 2025May 23, 2025

    • cytomarker

      Public
      Interactive design and validation of antibody panels using single-cell atlases
      R
      •
      Other
      •0•4•5•0•Updated Apr 11, 2025Apr 11, 2025

    • 2025_isomeric

      Public
      Code implementing ISOMERIC
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 7, 2025Apr 7, 2025

    • 2023-cytomarkerpaper-analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 14, 2025Mar 14, 2025

    • starling

      Public
      Segmentation error aware clustering for multiplexed imaging
      Python
      •
      Other
      •2•19•8•6•Updated Jan 9, 2025Jan 9, 2025

    • starling_plots

      Public
      R
      •0•1•0•0•Updated Oct 31, 2024Oct 31, 2024

    • beyond_benchmarking_analyses

      Public
      R
      •
      GNU General Public License v3.0
      •0•7•1•0•Updated May 31, 2024May 31, 2024

    • ACB_I_II

      Public
      JavaScript
      •0•0•0•0•Updated May 16, 2024May 16, 2024

    • rdrop2

      Public
      Dropbox Interface from R
      R
      •
      Other
      •60•0•0•0•Updated Mar 25, 2024Mar 25, 2024

    • active-learning-benchmarking

      Public
      R
      •0•3•0•0•Updated Dec 18, 2023Dec 18, 2023

    • active-learning-benchmarking-archive

      Public
      R
      •0•0•0•0•Updated Oct 23, 2023Oct 23, 2023

    • HEB_RNASeq

      Public
      R
      •0•0•0•0•Updated Sep 21, 2023Sep 21, 2023

    • scvi-tools-skeleton

      Public template
      Template repository for creating novel models with scvi-tools
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•0•0•1•Updated Jun 5, 2023Jun 5, 2023

    • 2022_manatee_paper_analyses

      Public
      Code implementing MANATEE used for the analyses in the associated paper.
      Python
      •
      GNU General Public License v3.0
      •1•4•0•0•Updated May 30, 2023May 30, 2023

    • leader

      Public
      R
      •0•2•0•0•Updated May 30, 2023May 30, 2023

    • 2021_SCVAR

      Public
      Python
      •0•1•0•0•Updated Apr 4, 2023Apr 4, 2023

    • infercnv-snakemake

      Public
      R
      •0•0•1•0•Updated Mar 3, 2023Mar 3, 2023

    • inferorg

      Public
      inferorg: automatic inference and conversion of gene ID formats across organisms
      R
      •0•1•0•0•Updated Feb 13, 2022Feb 13, 2022

    • acdc

      Public
      Bug fixed version of acdc
      Python
      •1•1•0•0•Updated Aug 3, 2021Aug 3, 2021

    • taproom

      Public
      taproom: Tools for spAtial PROteOmics | 🍻 🖥
      R
      •
      Other
      •0•0•0•0•Updated Aug 3, 2021Aug 3, 2021

    • astir-manuscript

      Public
      Analysis code for "Automated assignment of cell identity from single-cellmultiplexed imaging and proteomic data"
      R
      •0•1•1•0•Updated Aug 3, 2021Aug 3, 2021

    • AstirRuntime

      Public
      Python
      •0•0•0•0•Updated Jul 29, 2021Jul 29, 2021