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    49 repositories

    • loompy

      Public
      Python implementation of the Loom file format - http://loompy.org
      Python
      •
      BSD 2-Clause "Simplified" License
      •37•141•39•2•Updated Dec 16, 2024Dec 16, 2024

    • oligopy

      Public
      Python
      •2•2•0•1•Updated Sep 23, 2024Sep 23, 2024

    • fetal_brain_multiomics

      Public
      Supplementary files and notebooks to recreate figures.
      HTML
      •
      BSD 2-Clause "Simplified" License
      •1•15•0•0•Updated Sep 9, 2024Sep 9, 2024

    • developing-human-brain

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•28•12•0•Updated Aug 15, 2024Aug 15, 2024

    • FISHscale

      Public
      Spatial analysis of FISH data
      Jupyter Notebook
      •9•29•5•0•Updated May 31, 2024May 31, 2024

    • shoji

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•6•1•0•Updated May 28, 2024May 28, 2024

    • chromograph

      Public
      Camiel's scATAC-seq analysis pipeline
      Python
      •1•10•0•0•Updated Apr 15, 2024Apr 15, 2024

    • pysmFISH_auto

      Public
      Version of the pysmFISH pipeline that run without human in the loop
      Jupyter Notebook
      •
      MIT License
      •4•6•0•0•Updated Mar 29, 2024Mar 29, 2024

    • cytograph-shoji

      Public
      Jupyter Notebook
      •0•4•1•0•Updated Mar 17, 2024Mar 17, 2024

    • adult-human-brain

      Public
      Cytograph version used for adult human-brain analysis
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •14•76•10•0•Updated Feb 29, 2024Feb 29, 2024

    • MXII-valve

      Public
      MX Series II actuated valve
      Python
      •
      MIT License
      •0•4•0•0•Updated Feb 21, 2024Feb 21, 2024

    • cytograph-dev

      Public
      Algorithms for analysis of very large single-cell RNA-seq datasets
      Jupyter Notebook
      •0•0•0•0•Updated Jan 18, 2024Jan 18, 2024

    • glioblastoma_spatial

      Public
      Repository for Glioblastoma EEL-FISH data and code
      Jupyter Notebook
      •0•3•0•0•Updated Sep 1, 2023Sep 1, 2023

    • STspace

      Public
      A novel machine learning pipeline to analyse spatial transcriptomics data
      Python
      •
      Other
      •28•1•0•0•Updated Jun 18, 2023Jun 18, 2023

    • auto-annotation

      Public
      Computer-readable annotation for cell types and states
      0•1•2•0•Updated Jun 13, 2023Jun 13, 2023

    • cytograph2

      Public
      Python
      •0•14•1•0•Updated Feb 21, 2023Feb 21, 2023

    • Py_TC-720

      Public
      Python library to control the TC-720 temperature controller
      Python
      •
      MIT License
      •8•2•1•0•Updated Jan 30, 2023Jan 30, 2023

    • flamemaps

      Public
      Demo page for flame maps
      JavaScript
      •0•2•4•16•Updated Dec 7, 2022Dec 7, 2022

    • auto-annotation-ah

      Public
      Auto-annotations for analysis of the adult human brain
      2•5•1•0•Updated Sep 28, 2022Sep 28, 2022

    • ROBOFISH

      Public
      Control and installation of a cyclic smFISH robot
      Python
      •
      MIT License
      •0•1•0•0•Updated Aug 10, 2022Aug 10, 2022

    • BoneFight

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•8•0•0•Updated Nov 1, 2021Nov 1, 2021

    • tecancavro

      Public
      Python package to control Tecan Cavro OEM syringe pumps
      JavaScript
      •
      Other
      •18•0•0•0•Updated Oct 16, 2021Oct 16, 2021

    • Oasis_chiller

      Public
      Python library to control the Solid State Oasis recirculating chillers for temperature control.
      Python
      •
      MIT License
      •0•2•0•0•Updated Oct 16, 2021Oct 16, 2021

    • ThermoCube

      Public
      Python library for control of the Solid State ThermoCube recirculating chiller.
      Python
      •
      MIT License
      •1•1•0•0•Updated Oct 16, 2021Oct 16, 2021

    • cytograph

      Public
      Algorithms for single-cell analysis
      Python
      •5•29•1•0•Updated Jul 19, 2021Jul 19, 2021

    • auto-annotation-md

      Public
      Auto-annotations from Mouse brain development
      6•12•2•1•Updated Jul 11, 2020Jul 11, 2020

    • punchcards

      Public
      what you need to automate a loom
      0•0•0•0•Updated Jul 1, 2020Jul 1, 2020

    • colormetric-plate-scanner

      Public
      Code to find the test result of a color-metric LAMP assay on a flat-bed scanner.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 15, 2020Apr 15, 2020

    • starfish

      Public
      starfish: unified pipelines for image-based transcriptomics
      Python
      •
      MIT License
      •68•0•0•0•Updated Feb 27, 2020Feb 27, 2020

    • loom-viewer

      Public
      Tool for sharing, browsing and visualizing single-cell data stored in the Loom file format
      JavaScript
      •
      BSD 2-Clause "Simplified" License
      •6•35•44•1•Updated Aug 19, 2019Aug 19, 2019