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@cellgeni

Cellular Genetics Informatics

Wellcome Sanger Institute

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  1. STARsolo STARsolo Public

    wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq

    Shell 42 5

  2. reprocess_public_10x reprocess_public_10x Public

    Scripts to help get fastqs

    Shell 12 3

  3. c2l c2l Public

    Set of scripts to run cell2location on farm

    Jupyter Notebook

  4. cellatac cellatac Public

    Sanger Cellular Genetics single-cell ATAC-seq pipeline.

    Nextflow 10 6

  5. notebooks notebooks Public

    Cellular Genetics Informatics Notebooks

    HTML 20 12

  6. nf-cellbender nf-cellbender Public

    Nextflow implementation of Cellbender

    R

Repositories

Showing 10 of 80 repositories
  • nf-irods-to-fastq Public

    Get CRAMs from iRODS and convert them to FASTQ

    cellgeni/nf-irods-to-fastq’s past year of commit activity
    Nextflow 0 MIT 2 0 0 Updated Sep 19, 2024
  • farmer Public

    Slack bot that tells you the status of your LSF jobs

    cellgeni/farmer’s past year of commit activity
    Python 0 AGPL-3.0 0 0 0 Updated Sep 16, 2024
  • celltypist_census Public

    This repo includes the notebooks to test CellTypist by using the datasets downloaded from CELLxGENE portal by using Census.

    cellgeni/celltypist_census’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Sep 16, 2024
  • nf-reprocessing-public-10x Public

    Nextflow pipeline of Alex's reprocessing scripts

    cellgeni/nf-reprocessing-public-10x’s past year of commit activity
    Shell 0 GPL-3.0 0 0 0 Updated Sep 16, 2024
  • alignment_HE_DAPI Public

    multimodal alignment H&E RGB images to DAPI one channel images

    cellgeni/alignment_HE_DAPI’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 16, 2024
  • nf-starsolo Public

    Our STARsolo repo but designed for Nextflow Tower

    cellgeni/nf-starsolo’s past year of commit activity
    Shell 0 GPL-3.0 0 0 0 Updated Sep 16, 2024
  • various_cellrangers Public

    Various Cellranger Scripts used for different version etc

    cellgeni/various_cellrangers’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Sep 16, 2024
  • cellxgene_curation Public
    cellgeni/cellxgene_curation’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Sep 16, 2024
  • tracer-utils Public

    This repository contains scripts for running the Teichlab/tracer package.

    cellgeni/tracer-utils’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Sep 16, 2024
  • nf-scautoqc Public

    Nextflow implementation of scAutoQC pipeline

    cellgeni/nf-scautoqc’s past year of commit activity
    Python 1 GPL-3.0 0 0 0 Updated Sep 16, 2024
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