Cellular Genetics Informatics

sceasy

A package to help convert different single-cell data formats to each other

STARsolo

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

schard

reticulate-free single cell format conversion

reprocess_public_10x

Scripts to help get fastqs

cellatac

Sanger Cellular Genetics single-cell ATAC-seq pipeline.

rnaseq

Fast RNAseq pipeline

cellxgene

An interactive explorer for single-cell transcriptomics data

cellbender

Repo containing scripts for running cellbender

cellranger_cite_hash

Processing CITE-seq and cell hashing datasets with Cell Ranger

docs

CellGen IT documentation

c2l

Set of scripts to run cell2location on farm

celltypist_census

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

cellxgene_curation

nf-cellbender

Nextflow implementation of Cellbender

nf-starsolo

Our STARsolo repo but designed for Nextflow Tower

bulk_rnaseq

Wrapper scripts for convenient processing of bulk RNA-seq experiments

dockage

Cellgeni Docker files

grnboost2-configuration

Repository for storing general use configuration files for grnboost2

guitar

Get, merge & tar cram files with the same brush.

nf-demultiplex

Our Souporcell repo but for Nextflow Tower

nf-irods-to-fastq

Get CRAMs from iRODS and convert them to fastq

nf-reprocessing-public-10x

Nextflow pipeline of Alex's reprocessing scripts

nf-velocyto

Our Velocyto repo but for Nextflow Tower

notebook-snippets

A repository for cellular genetics informatics scientists to upload their notebooks to

references

souporcell

Repo containing our scripts for running souporcell

tracer-utils

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

various_cellrangers

Various Cellranger Scripts used for different version etc

velocyto

Cellgeni velocyto pipeline

vsn-pipelines

Forked repository of vib-singlecell-nf/vsn-pipelines to work on Sanger HPC