Description

Identify singlets, doublets and negative cells from multiplexing experiments. Annotate singlets by tags.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

seurat_object{:bash}

:file

A .rds file containing the seurat object. Assumes that the hash tag oligo (HTO) data has been added and normalized.

assay{:bash}

:string

Name of the Hashtag assay, usually called “HTO” by default. Use the custom name if the assay has been named differently.

Output

name:type
description
pattern

params{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*_params_multiseqdemux.csv{:bash}

:file

The used parameters to call MULTIseqDemux in the R-Script.

_params_multiseqdemux.csv

results{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*_res_multiseqdemux.csv{:bash}

:file

Resuls of MULTIseqDemux.

_res_multiseqdemux.csv

rds{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*_multiseqdemux.rds{:bash}

:file

SeuratObject saved as RDS.

_multiseqdemux.rds

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

multiseqdemux
MIT

MULTIseqDemux is the demultiplexing module of Seurat, which demultiplex samples based on data from cell hashing.

satijalab.org/seurat/reference/multiseqdemux https://github.com/satijalab/seurat 10.1038/s41592-019-0433-8
maintainer
Github user LuisHeinzlmeier
get in touch
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