Description

Demultiplexing cell nucleus hashing data, using the estimated antibody background probability.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

input_raw_gene_bc_matrices_h5{:bash}

:string

Path to file containing input raw RNA expression matrix in 10x hdf5 format pattern: ”*.{h5}”

input_hto_csv_file{:bash}

:string

Path to file containing input HTO (antibody tag) count matrix in CSV format.

*.{csv}

output_name{:bash}

:string

Output name. All outputs will use it as the prefix.

generate_gender_plot{:bash}

:string

Generate violin plots using gender-specific genes (e.g. Xist). It is a comma-separated list of gene names.

genome{:bash}

:string

Reference genome name. If not provided, the tools infers it from the expression matrix file

generate_diagnostic_plots{:bash}

:string

Generate diagnostic plots, including the background/signal between HTO counts, estimated background probabilities, HTO distributions.

Output

name:type
description
pattern

zarr{:bash}

meta{:bash}

:map

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

*_demux.zarr.zip{:bash}

:file

RNA expression matrix with demultiplexed sample identities in Zarr format.

*_demux.zarr.zip

out_zarr{:bash}

meta{:bash}

:map

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

*.out.demuxEM.zarr.zip{:bash}

:file

DemuxEM-calculated results in Zarr format, containing two datasets, one for HTO and one for RNA.

*.out.demuxEM.zarr.zip

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

demuxem
BSD-3-clause

DemuxEM is the demultiplexing module of Pegasus, which works on cell-hashing and nucleus-hashing genomics data.

demuxEM.readthedocs.io https://github.com/lilab-bcb/pegasus/tree/master 10.1038/s41467-019-10756-2
maintainers
Github user mari-ga
Github user maxozo
Github user wxicu
Github user Zethson
get in touch
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