velocity/scvelo
Description
No description provided.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Velocyto loom file. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output directory. If it does not exist, will be created. |
--output_compression | string | The compression format to be used on the output h5mu object. |
Filtering and normalization
Name | Type & Properties | Description |
|---|---|---|
--min_counts | integer | Minimum number of counts required for a gene to pass filtering (spliced). |
--min_counts_u | integer | Minimum number of counts required for a gene to pass filtering (unspliced). |
--min_cells | integer | Minimum number of cells expressed required to pass filtering (spliced). |
--min_cells_u | integer | Minimum number of cells expressed required to pass filtering (unspliced). |
--min_shared_counts | integer | Minimum number of counts (both unspliced and spliced) required for a gene. |
--min_shared_cells | integer | Minimum number of cells required to be expressed (both unspliced and spliced). |
--n_top_genes | integer | Number of genes to keep. |
--log_transform | boolean | Do not log transform counts. |
Fitting parameters
Name | Type & Properties | Description |
|---|---|---|
--n_principal_components | integer | Number of principal components to use for calculating moments. |
--n_neighbors | integer | Number of neighbors to use. First/second-order moments are computed for each cell across its nearest neighbors, where the neighbor graph is obtained from euclidean distances in PCA space. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output"
log_transform: [ true ]
n_neighbors: [ 30 ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision 1.0.2 \
-main-script target/nextflow/velocity/scvelo/main.nf \
-params-file params.yaml Relationships
Used by
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Current component
velocity/scveloopenpipeline 1.0.2
Uses
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