Description

Generating cell hashing calls from a matrix of count data.

Input

name:type
description
pattern

meta

:map

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

hto_matrix

:file

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

runEmptyDrops

:boolean

Run EmptyDrops() before hashedDrops() (“TRUE”) or not (“FALSE”).

rna_matrix

:file

Path to RNA count matrix, which is only uses if runEmptyDrops == “TRUE”.

Output

name:type
description
pattern

empty_drops_plot

meta

:map

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

*_emptyDrops.png

:file

EmptyDrops results plot

_emptyDrops.png

empty_drops_csv

meta

:map

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

*_emptyDrops.csv

:file

EmptyDrops results in CSV format

_emptyDrops.csv

empty_drops_rds

meta

:map

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

*_emptyDrops.rds

:file

EmptyDrops results in RDS format

_emptyDrops.rds

results

meta

:map

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

*_results_hasheddrops.csv

:file

HashedDrops results

_results_hasheddrops.csv

id_to_hash

meta

:map

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

*_id_to_hash.csv

:file

A table mapping integer indices used by hashedDrops results (e.g. the column Best or Second) to HTO names (or combinations of HTO names joined with + if combinations is speficied in ext.args).

_id_to_hash.csv

rds

meta

:map

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

*_hasheddrops.rds

:file

HashedDrops results in RDS format

_hasheddrops.rds

plot

meta

:map

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

*_plot_hasheddrops.png

:file

HashedDrops plot

_plot_hasheddrops.png

params

meta

:map

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

*_params_hasheddrops.csv

:file

The used parameters to call hashedDrops() in the R-Script.

_params_hasheddrops.csv

versions

versions.yml

:file

File containing software versions.

Tools

hasheddrops
GPL-3

Demultiplex cell barcodes into their samples of origin based on the most abundant hash tag oligo (HTO). Also identify potential doublets based on the presence of multiple significant HTOs.

rdrr.io/github/MarioniLab/DropletUtils/man/hashedDrops https://github.com/MarioniLab/DropletUtils 10.18129/B9.bioc.DropletUtils
maintainer
Github user LuisHeinzlmeier
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