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@cellgeni Cellular Genetics Informatics

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    96 repositories

    • snippets

      Public
      A repository for cellular genetics informatics scientists to upload their notebooks to
      Python
      •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

    • reprocess_public_10x

      Public
      Scripts to help get fastqs
      Shell
      •
      GNU General Public License v3.0
      •3•13•0•1•Updated Dec 19, 2024Dec 19, 2024

    • alignment_HE_DAPI

      Public
      multimodal alignment H&E RGB images to DAPI one channel images
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • nf-fgwas

      Public
      Nextflow implementation of fGWAS
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Dec 17, 2024Dec 17, 2024

    • visutils

      Public
      set of function for qc and visualization of Visium data
      R
      •
      MIT License
      •0•2•0•0•Updated Dec 17, 2024Dec 17, 2024

    • schard-py

      Public
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • reprocess_irods_upload

      Public
      A repo with collection of scripts and notebooks which where used to validate and upload datasets to IRODS
      Jupyter Notebook
      •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • docs

      Public
      CellGen IT documentation
      docswikireadthedocssanger
      MIT License
      •4•1•0•0•Updated Dec 12, 2024Dec 12, 2024

    • nf-scsajr

      Public
      single cell alternative splicing
      R
      •0•0•0•0•Updated Dec 10, 2024Dec 10, 2024

    • omero-scripts

      Public
      0•0•0•0•Updated Dec 9, 2024Dec 9, 2024

    • schard

      Public
      reticulate-free single cell format conversion
      R
      •
      GNU General Public License v3.0
      •4•99•2•0•Updated Dec 6, 2024Dec 6, 2024

    • nf-atac

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 2, 2024Dec 2, 2024

    • farmer

      Public
      Slack bot that tells you the status of your LSF jobs 🧑‍🌾
      Python
      •
      GNU Affero General Public License v3.0
      •0•3•0•0•Updated Nov 29, 2024Nov 29, 2024

    • cloupe

      Public
      Cloupe reader
      readersingle-cellloupe10x-genomics
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•0•2•0•Updated Nov 29, 2024Nov 29, 2024

    • webatlas-pipeline

      Public
      A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
      Python
      •
      MIT License
      •10•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • visium_vistools

      Public
      visualisation tools for Visium outputs
      Jupyter Notebook
      •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • nf-scautoqc

      Public
      Nextflow implementation of scAutoQC pipeline
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Nov 22, 2024Nov 22, 2024

    • nf-irods-to-fastq

      Public
      Get CRAMs from iRODS and convert them to FASTQ
      Nextflow
      •
      MIT License
      •2•1•0•0•Updated Nov 21, 2024Nov 21, 2024

    • nf-demultiplex

      Public
      Our Souporcell repo but for Nextflow Tower
      Nextflow
      •
      MIT License
      •0•0•1•0•Updated Nov 20, 2024Nov 20, 2024

    • napari-large-3d-vis

      Public
      napari plugin which allows to visualize any size 3D volumetric image without exceeding maximum allowed RAM size
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

    • modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •735•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • jupyter-images

      Public
      Cellular Genetics Informatics Docker Images for Jupyter
      Dockerfile
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Nov 5, 2024Nov 5, 2024

    • GBM-stuff

      Public
      Storing the scripts for use in the GBM project
      Java
      •
      MIT License
      •0•1•1•0•Updated Nov 5, 2024Nov 5, 2024

    • multiome-pipeline

      Public
      0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • c2l

      Public
      Set of scripts to run cell2location on farm
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Oct 30, 2024Oct 30, 2024

    • cells2visium

      Public
      segmenting H&E images from Visium to assign each visium spot to the number of cell, occupancy and other morphological features of cells
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 29, 2024Oct 29, 2024

    • SNP_tools

      Public
      storage for the tools for SNP projects we use
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 23, 2024Oct 23, 2024

    • dockage

      Public
      Cellgeni Docker files
      Dockerfile
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated Oct 22, 2024Oct 22, 2024

    • image_registration_tools

      Public
      tools for image registration
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

    • unwrap_CNS

      Public
      Truing visium spots of CNS from Embryo
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024