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.
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 1.0.4 \
-main-script target/nextflow/transform/regress_out/main.nf \
-params-file params.yaml Name | Type & Properties |
|---|---|
--input | file required |
--output -o | file required output |
--output_compression | string |
--modality | string |
--obs_keys | string multiple |