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10xcellranger

RNAseq pipeline for droplet based protocols

asthma

Teichlab asthma app

atacseq

Analysis pipeline for ATACseq data using Nextflow

atacseq-1

UNDER CONSTRUCTION: ATAC-seq peak-calling and differential analysis pipeline.

batchbench

bulk_rnaseq

Wrapper scripts for convenient processing of bulk RNA-seq experiments

c2l

Set of scripts to run cell2location on farm

cbdemux

Demultiplex bam files on CB field and compute rudimentary per-sample QC

cellatac

Sanger Cellular Genetics single-cell ATAC-seq pipeline.

cellbender

Repo containing scripts for running cellbender

cellgeni.github.io

https://cellgeni.github.io/

cellranger_cite_hash

Processing CITE-seq and cell hashing datasets with Cell Ranger

celltypist_census

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

cellxgene

An interactive explorer for single-cell transcriptomics data

cellxgene_curation

chipseq

Nextflow ChIP-seq Best Practise analysis pipeline

cytokine

dockage

Cellgeni Docker files

docker-jupyter

Docker image for the Cellular Genetics Informatics JupyterHub

docs

CellGen IT documentation

dropest

DropEst NF analysis pipeline

forecast

Computational prediction of editing outcomes resulting from Cas9-induced double strand breaks

gdown.pl

Google Drive direct download of big files

grnboost2-configuration

Repository for storing general use configuration files for grnboost2

guitar

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

hubmap-image-tools

Testing image analysis tools for HuBMAP

imaging-experiments-tracker

A service for tracking imaging experiments in Cellular Genetics Programme

imtr-pipeline-runner

A web service to check exported datasets and start imaging pipelines on the imaging nodes

irods

Dockerfile for iRods docker image

isee-shiny

Collection of dockerfiles for paper supporting websites