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@cellgeni Cellular Genomics Informatics

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    115 repositories

    • nf-cellbender

      Public
      Nextflow implementation of Cellbender
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 23, 2025Jul 23, 2025

    • nf-scVI-metrics

      Public
      Grid search to optimise hyperparameters for scVI
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 23, 2025Jul 23, 2025

    • webatlas-app

      Public
      An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.
      JavaScript
      •
      MIT License
      •4•0•0•0•Updated Jul 21, 2025Jul 21, 2025

    • iranger

      Public
      Read 10x analysis from iRODS
      Python
      •
      GNU Affero General Public License v3.0
      •0•3•0•0•Updated Jul 21, 2025Jul 21, 2025

    • nf-modules

      Public
      Python
      •
      MIT License
      •0•0•0•1•Updated Jul 17, 2025Jul 17, 2025

    • ovary

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 15, 2025Jul 15, 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•1•1•Updated Jul 15, 2025Jul 15, 2025

    • nf-demultiplex

      Public
      Our Souporcell repo but for Nextflow Tower
      Nextflow
      •
      MIT License
      •0•0•1•0•Updated Jul 15, 2025Jul 15, 2025

    • farm-course

      Public
      Materials for farm-course organised by cellgenIT
      Shell
      •0•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • schard

      Public
      reticulate-free single cell format conversion
      R
      •
      GNU General Public License v3.0
      •11•173•0•0•Updated Jul 8, 2025Jul 8, 2025

    • nf-scsajr

      Public
      single cell alternative splicing
      R
      •0•2•0•0•Updated Jul 8, 2025Jul 8, 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 Jul 8, 2025Jul 8, 2025

    • scsajr

      Public
      R package for nf-scsajr
      HTML
      •
      Other
      •0•2•0•0•Updated Jul 8, 2025Jul 8, 2025

    • dockage

      Public
      Cellgeni Docker files
      Dockerfile
      •
      GNU Affero General Public License v3.0
      •0•2•0•0•Updated Jul 7, 2025Jul 7, 2025

    • modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •883•0•0•0•Updated Jul 4, 2025Jul 4, 2025

    • docs

      Public
      CellGen IT documentation
      docswikireadthedocssanger
      MIT License
      •4•1•0•0•Updated Jul 2, 2025Jul 2, 2025

    • nf-irods-to-fastq

      Public
      Get CRAMs from iRODS and convert them to FASTQ
      Nextflow
      •
      MIT License
      •2•2•3•0•Updated Jun 30, 2025Jun 30, 2025

    • nf-cellsnplite

      Public
      Nextflow
      •0•0•0•0•Updated Jun 24, 2025Jun 24, 2025

    • nf-scautoqc

      Public
      Nextflow implementation of scAutoQC pipeline
      Python
      •
      GNU General Public License v3.0
      •0•10•0•0•Updated Jun 24, 2025Jun 24, 2025

    • visutils

      Public
      set of function for qc and visualization of Visium data
      R
      •
      MIT License
      •0•2•0•0•Updated Jun 13, 2025Jun 13, 2025

    • reprocess_public_10x

      Public
      Scripts to help get fastqs
      Shell
      •
      GNU General Public License v3.0
      •3•14•2•1•Updated Jun 10, 2025Jun 10, 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 Jun 10, 2025Jun 10, 2025

    • bulk_rnaseq

      Public
      Wrapper scripts for convenient processing of bulk RNA-seq experiments
      Shell
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated Jun 9, 2025Jun 9, 2025

    • STARsolo

      Public
      wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
      Shell
      •
      GNU General Public License v3.0
      •7•60•2•0•Updated Jun 6, 2025Jun 6, 2025

    • hackathon

      Public
      Python
      •0•0•0•0•Updated May 29, 2025May 29, 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 May 15, 2025May 15, 2025

    • xenium_vistools

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

    • nf-metacells

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

    • clij2-fft

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

    • OMERO_tools

      Public
      Python
      •0•1•0•0•Updated Apr 29, 2025Apr 29, 2025