Cellular Genetics Informatics (@cellgeni)
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cellgeni

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Top repositories

1

sceasy

A package to help convert different single-cell data formats to each other
R
377
star
2

batchbench

R
46
star
3

notebooks

Cellular Genetics Informatics Notebooks
HTML
15
star
4

STARsolo

wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
Shell
15
star
5

cellatac

Sanger Cellular Genetics single-cell ATAC-seq pipeline.
Nextflow
10
star
6

rnaseq

Fast RNAseq pipeline
Groovy
8
star
7

nf-workshop

Nextflow workshop at the Sanger Institute
Shell
7
star
8

reprocess_public_10x

Scripts to help get fastqs
Shell
6
star
9

nf-server

A server application for running Nextlfow workflows
Python
4
star
10

10xcellranger

RNAseq pipeline for droplet based protocols
Groovy
2
star
11

cellbender

Repo containing scripts for running cellbender
R
2
star
12

nf-scautoqc

Nextflow implementation of scAutoQC pipeline
Python
1
star
13

jupyter-images

Cellular Genetics Informatics Docker Images for Jupyter
Dockerfile
1
star
14

nf-introduction

An introduction to Nextflow, focussed on files and channels
Nextflow
1
star
15

docs

CellGen IT documentation
1
star
16

asthma

Teichlab asthma app
R
1
star
17

docker-jupyter

Docker image for the Cellular Genetics Informatics JupyterHub
Dockerfile
1
star
18

cellranger_cite_hash

Processing CITE-seq and cell hashing datasets with Cell Ranger
Shell
1
star
19

visium2cells

segmenting H&E images from Visium to assign each visium spot to the number of cell, occupancy and other morphological features of cells
Python
1
star
20

GBM-stuff

Storing the scripts for use in the GBM project
Java
1
star
21

FORECasT

Computational prediction of editing outcomes resulting from Cas9-induced double strand breaks
JavaScript
1
star