transform/regress_out

Description

Regress out (mostly) unwanted sources of variation.
Uses simple linear regression. This is inspired by Seurat's regressOut function in R [Satija15].
Note that this function tends to overcorrect in certain circumstances as described in issue theislab/scanpy#526.
See https://github.com/theislab/scanpy/issues/526.

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'  
output: "$id.$key.output"  
modality: [ "rna" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.0 \  
  -main-script target/nextflow/transform/regress_out/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input	file required	Input h5mu file
--output -o	file required output	Output h5mu file.
--modality	string	Which modality (one or more) to run this component on.
--obs_keys	string multiple	Which .obs keys to regress on.
--input_layer	string	The layer of the adata object to regress on. If not provided, the X attribute of the adata object will be used.
--output_layer	string	The layer of the adata object containing the regressed count data. If not provided, the X attribute of the adata object will be used.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--input

file

required

--output

-o

file

required

output

--modality

string

--obs_keys

string

multiple

--input_layer

string

--output_layer

string

--output_compression

string