Projects in Awesome Lists by cellgeni
A curated list of projects in awesome lists by cellgeni .
https://github.com/cellgeni/sceasy
A package to help convert different single-cell data formats to each other
Last synced: 23 Jan 2026
https://github.com/cellgeni/schard
reticulate-free single cell format conversion
Last synced: 23 Jan 2026
https://github.com/cellgeni/notebooks
Cellular Genetics Informatics Notebooks
Last synced: 23 Jan 2026
https://github.com/cellgeni/reprocess_public_10x
Scripts to help get fastqs
Last synced: 23 Jan 2026
https://github.com/cellgeni/cellatac
Sanger Cellular Genetics single-cell ATAC-seq pipeline.
10x-genomics atac-seq atac-seq-pipeline nextflow-pipeline single-cell-atac-seq
Last synced: 23 Jan 2026
https://github.com/cellgeni/nf-scautoqc
Nextflow implementation of scAutoQC pipeline
Last synced: 21 Feb 2026
https://github.com/cellgeni/cellranger_cite_hash
Processing CITE-seq and cell hashing datasets with Cell Ranger
Last synced: 23 Jan 2026
https://github.com/cellgeni/farmer
Slack bot that tells you the status of your LSF jobs 🧑🌾
Last synced: 23 Jan 2026
https://github.com/cellgeni/c2l
Set of scripts to run cell2location on farm
Last synced: 23 Jan 2026
https://github.com/cellgeni/visutils
set of function for qc and visualization of Visium data
Last synced: 23 Jan 2026
https://github.com/cellgeni/nf-irods-to-fastq
Get CRAMs from iRODS and convert them to FASTQ
Last synced: 23 Jan 2026
https://github.com/cellgeni/gbm-stuff
Storing the scripts for use in the GBM project
Last synced: 23 Jan 2026
https://github.com/cellgeni/jupyter-images
Cellular Genetics Informatics Docker Images for Jupyter
Last synced: 23 Jan 2026
https://github.com/cellgeni/cloupe
Cloupe reader
10x-genomics loupe reader single-cell
Last synced: 23 Jan 2026
https://github.com/cellgeni/nf-atac
Pipeline to process sc-ATAC data with pyCistopic
atac-seq bioinformatics multiome nextflow pipeline python single-cell single-cell-atac-seq single-cell-multiomics
Last synced: 23 Jan 2026
https://github.com/cellgeni/napari-large-3d-vis
napari plugin which allows to visualize any size 3D volumetric image without exceeding maximum allowed RAM size
Last synced: 23 Jan 2026
https://github.com/cellgeni/snippets
A repository for cellular genetics informatics scientists to upload their notebooks to
Last synced: 23 Jan 2026
https://github.com/cellgeni/nf-scvi-metrics
Grid search to optimise hyperparameters for scVI
Last synced: 23 Jan 2026
https://github.com/cellgeni/farm-course
Materials for farm-course organised by cellgenIT
Last synced: 23 Jan 2026
https://github.com/cellgeni/various_cellrangers
Various Cellranger Scripts used for different version etc
Last synced: 23 Jan 2026
https://github.com/cellgeni/snp_tools
storage for the tools for SNP projects we use
Last synced: 23 Jan 2026
https://github.com/cellgeni/celltypist_census
This repo includes the notebooks to test CellTypist by using the datasets downloaded from CELLxGENE portal by using Census.
Last synced: 23 Jan 2026
https://github.com/cellgeni/nf-demultiplex
Our Souporcell repo but for Nextflow Tower
Last synced: 23 Jan 2026
https://github.com/cellgeni/reprocess_irods_upload
A repo with collection of scripts and notebooks which where used to validate and upload datasets to IRODS
Last synced: 23 Jan 2026
https://github.com/cellgeni/nf-cellbender
Nextflow implementation of Cellbender
Last synced: 23 Jan 2026
https://github.com/cellgeni/nf-processed2irods
Pipeline to move processed datasets to irods
Last synced: 23 Jan 2026
https://github.com/cellgeni/nf-starsolo
Our STARsolo repo but designed for Nextflow Tower
Last synced: 23 Jan 2026
https://github.com/cellgeni/nf-reprocessing-public-10x
Nextflow pipeline of Alex's reprocessing scripts
Last synced: 23 Jan 2026
https://github.com/cellgeni/imaging-experiments-tracker
A service for tracking imaging experiments in Cellular Genetics Programme
Last synced: 23 Jan 2026
https://github.com/cellgeni/xenium_vistools
visualisation codes for Xenium experiments
Last synced: 23 Jan 2026
https://github.com/cellgeni/tracer-utils
This repository contains scripts for running the Teichlab/tracer package.
Last synced: 23 Jan 2026
https://github.com/cellgeni/omero-download
Download images from OMERO server
Last synced: 23 Jan 2026