cellgeni/batchbench

Stars
46
Rank 613,923 (Top 13 %)
Language
R
License
MIT License
Created over 5 years ago
Updated over 2 years ago

cellgeni/batchbench

cellgeni

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sceasy

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

notebooks

Cellular Genetics Informatics Notebooks

STARsolo

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

cellatac

Sanger Cellular Genetics single-cell ATAC-seq pipeline.

rnaseq

Fast RNAseq pipeline

nf-workshop

Nextflow workshop at the Sanger Institute

reprocess_public_10x

Scripts to help get fastqs

nf-server

A server application for running Nextlfow workflows

10xcellranger

RNAseq pipeline for droplet based protocols

cellbender

Repo containing scripts for running cellbender

nf-scautoqc

Nextflow implementation of scAutoQC pipeline

jupyter-images

Cellular Genetics Informatics Docker Images for Jupyter

nf-introduction

An introduction to Nextflow, focussed on files and channels

docs

CellGen IT documentation

asthma

Teichlab asthma app

docker-jupyter

Docker image for the Cellular Genetics Informatics JupyterHub

cellranger_cite_hash

Processing CITE-seq and cell hashing datasets with Cell Ranger

visium2cells

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

GBM-stuff

Storing the scripts for use in the GBM project

FORECasT

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