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@cellgeni Cellular Genetics Informatics

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    111 repositories

    • xenium_vistools

      Public
      visualisation codes for Xenium experiments
      Jupyter Notebook
      •0•0•0•0•Updated May 13, 2025May 13, 2025

    • nf-scautoqc

      Public
      Nextflow implementation of scAutoQC pipeline
      Python
      •
      GNU General Public License v3.0
      •0•6•0•0•Updated May 13, 2025May 13, 2025

    • nf-cellsnplite

      Public
      Nextflow
      •0•0•0•0•Updated May 12, 2025May 12, 2025

    • nf-atac

      Public
      Pipeline to process sc-ATAC data with pyCistopic
      pythonbioinformaticspipelinenextflowatac-seqsingle-cellsingle-cell-atac-seqsingle-cell-multiomicsmultiome
      Python
      •
      MIT License
      •0•1•0•0•Updated May 12, 2025May 12, 2025

    • ovary

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 8, 2025May 8, 2025

    • modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •854•0•0•0•Updated May 7, 2025May 7, 2025

    • dockage

      Public
      Cellgeni Docker files
      Dockerfile
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated May 6, 2025May 6, 2025

    • nf-modules

      Public
      Python
      •
      MIT License
      •0•0•0•1•Updated May 3, 2025May 3, 2025

    • visutils

      Public
      set of function for qc and visualization of Visium data
      R
      •
      MIT License
      •0•2•0•0•Updated May 1, 2025May 1, 2025

    • nf-metacells

      Public
      Python
      •0•0•0•0•Updated Apr 30, 2025Apr 30, 2025

    • clij2-fft

      Public
      10000 Jupyter Notebook
      •7•0•0•0•Updated Apr 29, 2025Apr 29, 2025

    • OMERO_tools

      Public
      Python
      •0•0•0•0•Updated Apr 29, 2025Apr 29, 2025

    • nf-scVI-metrics

      Public
      Grid search to optimise hyperparameters for scVI
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 25, 2025Apr 25, 2025

    • Image-ST

      Public
      A pipeline to generate count matrix for different spatial technologies. ISS/MERFISH-like data are decoded using PoSTcode
      Python
      •
      MIT License
      •1•1•0•0•Updated Apr 23, 2025Apr 23, 2025

    • nf-cellbender

      Public
      Nextflow implementation of Cellbender
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 17, 2025Apr 17, 2025

    • example-module-2

      Public
      Nextflow
      •0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

    • example-module-1

      Public
      Nextflow
      •0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

    • nf-reprocessing-public-10x

      Public
      Nextflow pipeline of Alex's reprocessing scripts
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • nf-velocyto

      Public
      Our Velocyto repo but for Nextflow Tower
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • nf-demultiplex

      Public
      Our Souporcell repo but for Nextflow Tower
      Nextflow
      •
      MIT License
      •0•0•1•0•Updated Apr 9, 2025Apr 9, 2025

    • nf-starsolo

      Public
      Our STARsolo repo but designed for Nextflow Tower
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • omeroimport

      Public
      Shell
      •0•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • snippets

      Public
      A repository for cellular genetics informatics scientists to upload their notebooks to
      Python
      •0•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • spatialxe

      Public
      Nextflow
      •
      MIT License
      •9•0•0•0•Updated Apr 8, 2025Apr 8, 2025

    • c2l

      Public
      Set of scripts to run cell2location on farm
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Apr 7, 2025Apr 7, 2025

    • STARsolo

      Public
      wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
      Shell
      •
      GNU General Public License v3.0
      •6•56•0•0•Updated Apr 3, 2025Apr 3, 2025

    • 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 Apr 1, 2025Apr 1, 2025

    • nf-scsajr

      Public
      single cell alternative splicing
      R
      •0•2•0•0•Updated Mar 31, 2025Mar 31, 2025

    • various_cellrangers

      Public
      Various Cellranger Scripts used for different version etc
      Shell
      •
      MIT License
      •0•0•0•0•Updated Mar 27, 2025Mar 27, 2025

    • bulk_rnaseq

      Public
      Wrapper scripts for convenient processing of bulk RNA-seq experiments
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 25, 2025Mar 25, 2025
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