Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

input_raw_gene_bc_matrices_h5 (string)

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

input_hto_csv_file (string)

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

*.{csv}

output_name (string)

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

generate_gender_plot (string)

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

genome (string)

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

generate_diagnostic_plots (string)

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

Output

Name (Type)
Description
Pattern

meta (map)

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

zarr (file)

RNA expression matrix with demultiplexed sample identities in Zarr format.

*_demux.zarr.zip

out_zarr (file)

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

*.out.demuxEM.zarr.zip

versions (file)

File containing software versions

versions.yml
maintainers
Github user mari-ga
Github user maxozo
Github user wxicu
Github user Zethson
get in touch
Ask a question on Slack Open an issue on GitHub

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