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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 43 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 1

  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 82 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 30, 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 30, 2024
  • fastapi_websocket_rpc Public Forked from permitio/fastapi_websocket_rpc

    ⚡ FASTAPI Websocket RPC- A fast and durable bidirectional JSON RPC channel over Websockets.

    cellgeni/fastapi_websocket_rpc’s past year of commit activity
    Python 1 MIT 24 0 0 Updated Sep 30, 2024
  • cloupe Public

    Cloupe reader

    cellgeni/cloupe’s past year of commit activity
    Jupyter Notebook 0 AGPL-3.0 0 0 0 Updated Sep 28, 2024
  • schard Public

    reticulate-free single cell format conversion

    cellgeni/schard’s past year of commit activity
    R 76 GPL-3.0 4 2 0 Updated Sep 27, 2024
  • dockage Public

    Cellgeni Docker files

    cellgeni/dockage’s past year of commit activity
    Dockerfile 0 AGPL-3.0 0 0 0 Updated Sep 26, 2024
  • reprocess_public_10x Public

    Scripts to help get fastqs

    cellgeni/reprocess_public_10x’s past year of commit activity
    Shell 12 GPL-3.0 3 1 0 Updated Sep 25, 2024
  • STARsolo Public

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

    cellgeni/STARsolo’s past year of commit activity
    Shell 43 GPL-3.0 5 0 0 Updated Sep 25, 2024
  • visium2cells Public

    segmenting H&E images from Visium to assign each visium spot to the number of cell, occupancy and other morphological features of cells

    cellgeni/visium2cells’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Sep 24, 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
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