Description

Generating cell hashing calls from a matrix of count data.

Input

name:type
description
pattern

meta{:bash}

:map

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

hto_matrix{:bash}

:file

Directory that contains the HTO matrix in a 10X format.

methods{:bash}

:string

Decides whether ‘RAW’, ‘CLUSTER’ OR ‘COMBINED’ should be selected as the call method.

preprocessing{:bash}

:string

Decides whether the HTO matrix should undergo a preprocessing step (‘TRUE’) or not (‘FALSE’).

Output

name:type
description
pattern

assignment{:bash}

meta{:bash}

:file

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

*_assignment_bff.csv{:bash}

:file

Contains the assignment results of demultiplexing.

assignment_bff.csv

metrics{:bash}

meta{:bash}

:file

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

*_metrics_bff.csv{:bash}

:file

Summary metrics will be written to this file.

_metrics_bff.csv

params{:bash}

meta{:bash}

:map

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

*_params_bff.csv{:bash}

:file

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

params_htodemux.csv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions.

versions.yml

Tools

bff
GPL-3

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.

rdrr.io/github/BimberLab/cellhashR/man/GenerateCellHashingCalls https://github.com/BimberLab/cellhashR 10.5281/zenodo.6402477
maintainer
Github user LuisHeinzlmeier
get in touch
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