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    99 repositories

    • iohub

      Public
      Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata
      pythonimage-metadatabioimagingndimensional-arraysome-zarrome-zarr-converter
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•32•32•6•Updated Dec 20, 2024Dec 20, 2024

    • ulc-malaria-autofocus

      Public
      A single-shot autofocus CNN for the Remoscope project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • remo-stats-utils

      Public
      This is a collection of statistics utilities used to support the Remoscope project at the Chan Zuckerberg Biohub San Francisco.
      machine-learningblooddiagnosticsmalariaedge-computinglow-costmalaria-detectionhematology
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • lfm-data-utilities

      Public
      A collection of auxiliary data processing tools used in the Remoscope project.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • shrimPy

      Public
      shrimPy: Smart High-throughput Robust Imaging & Measurement in Python
      multi-modal-imaginglightsheethigh-throughput-data-analysislabelfreehigh-throughput-imaging
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•8•30•2•Updated Dec 17, 2024Dec 17, 2024

    • czb-ui

      Public
      CZ Biohub's higher level components made with CZI's Science Design System Component Library.
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•12•1•Updated Dec 17, 2024Dec 17, 2024

    • proteinxlocation

      Public
      An interactive explorer for single-cell transcriptomics data
      JavaScript
      •
      MIT License
      •121•0•0•1•Updated Dec 12, 2024Dec 12, 2024

    • zebrahub-multiome-analysis

      Public
      A repository for scripts and notebooks to process and analyze single-cell Multiome datasets from early zebrafish embryos (zebrahub)
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•1•0•Updated Dec 10, 2024Dec 10, 2024

    • napari-plugins-docker

      Public
      Build a Napari image with common plugins
      Dockerfile
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • napari-iohub

      Public
      OME-Zarr viewer for napari with iohub as the I/O backend
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•8•1•Updated Nov 21, 2024Nov 21, 2024

    • comparison-RNAVelo

      Public
      Comparison of single-cell RNA Velocity methods in developmental contexts
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Nov 19, 2024Nov 19, 2024

    • zebrahub_analysis

      Public
      Analysis of single-cell single-embryo RNA seq data from the zebrafish developmental atlas Zebrahub.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•0•0•Updated Nov 16, 2024Nov 16, 2024

    • Organelle_IP_analyses_and_figures

      Public
      Jupyter notebooks for analysis and figures related to the native organelle IP paper
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•1•0•Updated Oct 28, 2024Oct 28, 2024

    • Rapid-QC-MS

      Public
      Realtime quality control for mass spectrometry data acquisition
      metabolomicsmass-spectrometryplotly-dash
      Python
      •
      Other
      •2•15•15•0•Updated Oct 24, 2024Oct 24, 2024

    • 2021-opencell-figures

      Public
      Public read-only repo for code and data related to the 2021 OpenCell preprint
      Jupyter Notebook
      •
      Other
      •1•5•2•0•Updated Sep 10, 2024Sep 10, 2024

    • random-walk-epidemic-model

      Public
      A random walk epidemic model.
      Jupyter Notebook
      •
      Other
      •1•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • sc2-guide-InSilicoSCR

      Public
      InSilico off-target screening for SC2 guides.
      Python
      •
      Other
      •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • covid19-transcriptomics-pathogenesis-diagnostics-results

      Public
      Jupyter Notebook
      •
      Other
      •7•5•0•0•Updated Sep 10, 2024Sep 10, 2024

    • EpiGen-COVID19

      Public
      Using both phylogenetic and time-series data from the COVID19 pandemic to estimate number of missing infections and predict forward epidemic trajectory.
      R
      •
      Other
      •1•4•0•0•Updated Sep 10, 2024Sep 10, 2024

    • bcell_pipeline

      Public
      Immcantation B-cell Repertoire Sequencing Pipeline adapted for Reflow
      R
      •
      Other
      •1•3•1•0•Updated Sep 10, 2024Sep 10, 2024

    • maca

      Public
      Command line utilities for RNA-sequencing data
      Python
      •
      Other
      •3•2•0•1•Updated Sep 10, 2024Sep 10, 2024

    • MIDAS

      Public
      Metagenomic Intra-Species Diversity Analysis (MIDAS)
      Python
      •
      MIT License
      •10•36•5•0•Updated Sep 3, 2024Sep 3, 2024

    • coPylot

      Public
      coPylot - microscope control
      instrument-controlpython
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•8•26•16•Updated Aug 27, 2024Aug 27, 2024

    • crispycrunch

      Public archive
      Web app for CRISPR experiment setup and analysis
      crisprpostgresdjangofastq-filesbiohub
      Python
      •
      MIT License
      •1•6•0•1•Updated Aug 23, 2024Aug 23, 2024

    • protoSpaceJAM

      Public
      CRISPR knock-in design at scale
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•7•9•0•Updated Aug 5, 2024Aug 5, 2024

    • yogo

      Public
      The "you only glance once" object detection model
      pytorchyoloobject-detection
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•11•5•4•Updated Jul 8, 2024Jul 8, 2024

    • protoSpaceJAM-portal

      Public
      Webserver allowing non-bioinformaticians to easily run protospaceJAM.
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jun 23, 2024Jun 23, 2024

    • GenoPrimer

      Public
      Automated primer design for genotyping CRISPR edited cells
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•2•0•Updated May 18, 2024May 18, 2024

    • DeepGenotype

      Public
      Calculate the outcome genotype frequencies in CRISPR genome editing experiments using deep sequencing reads.
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated May 18, 2024May 18, 2024

    • excellxgene

      Public
      JavaScript
      •
      MIT License
      •5•11•4•1•Updated Feb 23, 2024Feb 23, 2024