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jupyter-images

Cellular Genetics Informatics Docker Images for Jupyter

nf-cellbender

Nextflow implementation of Cellbender

nf-demultiplex

Our Souporcell repo but for Nextflow Tower

nf-introduction

An introduction to Nextflow, focussed on files and channels

nf-irods-to-fastq

Get CRAMs from iRODS and convert them to fastq

nf-login

A Nextflow controller pod for k8s cluster, with some additional utilities

nf-reprocessing-public-10x

Nextflow pipeline of Alex's reprocessing scripts

nf-server

A server application for running Nextlfow workflows

nf-starsolo

Our STARsolo repo but designed for Nextflow Tower

nf-velocyto

Our Velocyto repo but for Nextflow Tower

nf-workshop

Nextflow workshop at the Sanger Institute

notebook-snippets

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

notebooks

Cellular Genetics Informatics Notebooks

notebooks-base

Base docker image for CellGen JupyterHub

omero-wsi

patterns

A curated collections of Nextflow implementation patterns -- http://nextflow-io.github.io/patterns/index.html

pipeline-import

projman

Docker based JupyterHub project launcher for OpenStack

references

reprocess_public_10x

Scripts to help get fastqs

rnaseq

Fast RNAseq pipeline

rnaseq-nf

A pipeline for testing Kubernetes integration

rnaseq-old

RNASeq pipeline suitable for bulk and SmartSeq2 protocols

samples-tracker

Prototype for DNA samples tracking web application

sceasy

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

scfind

k8s config files for scfind application

schard

reticulate-free single cell format conversion

scmapindex

Nextflow pipeline for scmap index creation for a collection of SingleCellExperiment files

scrna.seq.course

Analysis of single cell RNA-seq data course

scrnaseq-genotyping

A selection of scripts to assign barcoded single cells to a likely donor given a sorted BAM file and a list of barcodes to consider.