Viash Hub

Description

Doublet detection using the Scrublet method (Wolock, Lopez and Klein, 2019).
The method tests for potential doublets by using the expression profiles of
cells to generate synthetic potential doubles which are tested against cells.
The method returns a "doublet score" on which it calls for potential doublets.

For the source code please visit https://github.com/AllonKleinLab/scrublet.

For 10x we expect the doublet rates to be:
Multiplet Rate (%) - # of Cells Loaded - # of Cells Recovered
~0.4% ~800 ~500
~0.8% ~1,600 ~1,000
~1.6% ~3,200 ~2,000
~2.3% ~4,800 ~3,000
~3.1% ~6,400 ~4,000
~3.9% ~8,000 ~5,000
~4.6% ~9,600 ~6,000
~5.4% ~11,200 ~7,000
~6.1% ~12,800 ~8,000
~6.9% ~14,400 ~9,000
~7.6% ~16,000 ~10,000

Arguments

Name	Type & Properties	Description
--input	file required	Input h5mu file
--modality	string
--layer	string	Input layer to use as data for calculating doublets. .X is used not specified.
--output	file output	Output h5mu file.
--output_compression	string	The compression format to be used on the output h5mu object.
--obs_name_filter	string	In which .obs slot to store a boolean array corresponding to which observations should be filtered out.
--do_subset	boolean_true	Whether to subset before storing the output.
--obs_name_doublet_score	string	Name of the doublet scores column in the obs slot of the returned object.
--min_counts	integer	The number of minimal UMI counts per cell that have to be present for initial cell detection.
--min_cells	integer	The number of cells in which UMIs for a gene were detected.
--min_gene_variablity_percent	double	Used for gene filtering prior to PCA. Keep the most highly variable genes (in the top min_gene_variability_pctl percentile), as measured by the v-statistic [Klein et al., Cell 2015].
--num_pca_components	integer	Number of principal components to use during PCA dimensionality reduction.
--distance_metric	string	The distance metric used for computing similarities.
--allow_automatic_threshold_detection_fail	boolean_true	When scrublet fails to automatically determine the double score threshold, allow the component to continue and set the output columns to NA.

Name

Type & Properties

--input

file

required

--modality

string

--layer

string

--output

file

output

--output_compression

string

--obs_name_filter

string

--do_subset

boolean_true

--obs_name_doublet_score

string

--min_counts

integer

--min_cells

integer

--min_gene_variablity_percent

double

--num_pca_components

integer

--distance_metric

string

--allow_automatic_threshold_detection_fail

boolean_true

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
output: "$id.$key.output.h5mu"  
obs_name_filter: [ "filter_with_scrublet" ]  
obs_name_doublet_score: [ "scrublet_doublet_score" ]  
min_counts: [ 2 ]  
min_cells: [ 3 ]  
min_gene_variablity_percent: [ 85 ]  
num_pca_components: [ 30 ]  
distance_metric: [ "euclidean" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.2 \  
  -main-script target/nextflow/filter/filter_with_scrublet/main.nf \  
  -params-file params.yaml

Relationships

Used by

1 relationships

workflows/rna/rna_singlesampleopenpipeline 1.0.2

Current component

filter/filter_with_scrubletopenpipeline 1.0.2

Uses

0 relationships

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