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@cellgeni Cellular Genomics Informatics

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    145 repositories

    • c2l

      Public
      Set of scripts to run cell2location on farm
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Sep 9, 2026Sep 9, 2026

    • dockage

      Public
      Cellular Genomics Informatics Dockerfiles
      Dockerfile
      •
      GNU Affero General Public License v3.0
      •1•3•0•0•Updated Sep 9, 2026Sep 9, 2026

    • nf-processed2irods

      Public
      Pipeline to move processed datasets to irods
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Sep 8, 2026Sep 8, 2026

    • validate-hierarchy

      Public
      Validate directory and iRODS collection hierarchies against a declarative YAML schema
      pythoncliirods
      pythoncliirods
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 8, 2026Sep 8, 2026

    • nf-modules

      Public
      Python
      •
      MIT License
      •0•1•0•2•Updated Sep 7, 2026Sep 7, 2026

    • nf-scsajr

      Public
      single cell alternative splicing
      R
      •0•2•0•0•Updated Sep 4, 2026Sep 4, 2026

    • alignment_HE_DAPI

      Public
      multimodal alignment H&E RGB images to DAPI one channel images
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Sep 4, 2026Sep 4, 2026

    • nf-reprocessing-public-10x

      Public
      Nextflow pipeline of Alex's reprocessing scripts
      Shell
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Sep 3, 2026Sep 3, 2026

    • STARsolo

      Public
      wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
      Shell
      •
      GNU General Public License v3.0
      •10•93•4•1•Updated Sep 3, 2026Sep 3, 2026

    • nf-scenicplus

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Sep 2, 2026Sep 2, 2026

    • explorer

      Public
      TypeScript
      •0•0•0•0•Updated Sep 1, 2026Sep 1, 2026

    • nf-irods-to-fastq

      Public
      Get CRAMs from iRODS and convert them to FASTQ
      Nextflow
      •
      MIT License
      •2•2•1•0•Updated Aug 28, 2026Aug 28, 2026

    • omero-download

      Public
      Download images from OMERO server
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Aug 26, 2026Aug 26, 2026

    • nf-cellbender

      Public
      Nextflow implementation of Cellbender
      R
      •
      MIT License
      •0•0•0•1•Updated Aug 20, 2026Aug 20, 2026

    • spatialdata-dissect

      Public
      Tissue-region detection and cropping tools for Xenium data in SpatialData objects.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 19, 2026Aug 19, 2026

    • AKOYA_analysis

      Public
      set of codes for analysis of sptaial proteomics datasets
      Jupyter Notebook
      •0•1•0•0•Updated Aug 11, 2026Aug 11, 2026

    • Image-ST

      Public
      A pipeline to generate count matrix for different spatial technologies. ISS/MERFISH-like data are decoded using PoSTcode
      Python
      •
      MIT License
      •3•5•0•0•Updated Aug 6, 2026Aug 6, 2026

    • OMERO_tools

      Public
      Python
      •0•2•0•0•Updated Jul 28, 2026Jul 28, 2026

    • cell_assignment

      Public
      assigning cells from different segmentations for xenium dataset
      Python
      •
      MIT License
      •0•1•0•0•Updated Jul 27, 2026Jul 27, 2026

    • nf-scVI-metrics

      Public
      Grid search to optimise hyperparameters for scVI
      Python
      •
      MIT License
      •2•4•1•1•Updated Jul 24, 2026Jul 24, 2026

    • pidgeon

      Public
      registration package
      Python
      •
      MIT License
      •0•1•0•0•Updated Jul 14, 2026Jul 14, 2026

    • nf-metacells

      Public
      Python
      •0•1•0•0•Updated Jul 10, 2026Jul 10, 2026

    • schard

      Public
      reticulate-free single cell format conversion
      R
      •
      GNU General Public License v3.0
      •16•220•0•0•Updated Jul 10, 2026Jul 10, 2026

    • nf-scautoqc

      Public
      Nextflow implementation of scAutoQC pipeline
      Python
      •
      GNU General Public License v3.0
      •0•12•1•1•Updated Jul 9, 2026Jul 9, 2026

    • nf-autoannotate

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Jul 1, 2026Jul 1, 2026

    • nf-upload2irods

      Public
      Pipeline for uploading files to iRODS system
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Jun 29, 2026Jun 29, 2026

    • visium_vistools

      Public
      visualisation tools for Visium outputs
      Jupyter Notebook
      •1•0•0•1•Updated Jun 23, 2026Jun 23, 2026

    • webatlas-pipeline

      Public
      A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
      Python
      •
      MIT License
      •13•0•0•0•Updated Jun 23, 2026Jun 23, 2026

    • bsubs

      Public
      LSF Submission examples
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jun 23, 2026Jun 23, 2026

    • iranger

      Public
      Read 10x analysis from iRODS
      Python
      •
      GNU Affero General Public License v3.0
      •0•4•0•0•Updated Jun 18, 2026Jun 18, 2026
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