create_pseudobulk/differential_expression

Description

Generation of pseudobulk samples from single-cell transcriptomics data,
by aggregating raw gene expression counts from individual cells to create
bulk-like expression profiles suitable for differential expression analysis
with methods designed for bulk differential expression analysis.
Note that this componentonly considers factors as explanatory variables,
and excludes covariates from the analysis.

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
aggregation_method: [ "sum" ]  
min_obs_per_sample: [ 30 ]  
random_state: [ 0 ]  
obs_cell_count: [ "n_cells" ]  
output: "$id.$key.output"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.2 \  
  -main-script target/nextflow/create_pseudobulk/differential_expression/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input h5mu file.
--modality	string	Which modality from the input MuData file to process.
--input_layer	string	Input layer to use. If None, X is used. This layer must contain raw counts.
--obs_label	string required	.obs field containing the variable to group on. Typically this field contains cell groups such as annotated cell types or clusters.
--obs_groups	string multiple	.obs fields containing the experimental condition(s) to create pseudobulk samples for.

Name

Type & Properties

--input

-i

file

required

--modality

string

--input_layer

string

--obs_label

string

required

--obs_groups

string

multiple

Arguments

Name	Type & Properties	Description
--aggregation_method	string	Method to aggregate the raw counts for pseudoreplicates. Either sum or mean.
--min_obs_per_sample	integer	Minimum number of cells per pseudobulk sample.
--random_state	integer	The random seed for sampling.
--obs_cell_count	string	The .obs field to store the number of observations per pseudobulk sample.

Name

Type & Properties

--aggregation_method

string

--min_obs_per_sample

integer

--random_state

integer

--obs_cell_count

string

Outputs

Name	Type & Properties	Description
--output	file required output	Output h5mu file containing the aggregated pseudobulk samples.
--output_compression	string	The compression format to be used on the output h5mu object.

Name

Type & Properties

--output

file

required

output

--output_compression

string