Lianapy

Performs LIANA integration based as described in https://github.com/saezlab/liana-py

Info

ID: lianapy
Namespace: interpret

Links

Source

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -main-script target/nextflow/interpret/lianapy/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
input: # please fill in - example: "path/to/file"
# output: "$id.$key.output.output"
output_compression: "gzip"
modality: "rna"
# layer: "foo"
groupby: "bulk_labels"
resource_name: "consensus"
gene_symbol: "gene_symbol"
expr_prop: 0.1
min_cells: 5
aggregate_method: "rra"
return_all_lrs: false
n_perms: 100

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -profile docker \
  -main-script target/nextflow/interpret/lianapy/main.nf \
  -params-file params.yaml

Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument group

Arguments

Name	Description	Attributes
--input	Input h5mu file	file, required
--output	Output h5mu file.	file, required
--output_compression		string, default: "gzip"
--modality		string, default: "rna"
--layer	Layer in anndata.AnnData.layers to use. If None, use mudata.mod[modality].X.	string
--groupby	The key of the observations grouping to consider.	string, default: "bulk_labels"
--resource_name	Name of the resource to be loaded and use for ligand-receptor inference.	string, default: "consensus"
--gene_symbol	Column name in var DataFrame in which gene symbol are stored.	string, default: "gene_symbol"
--expr_prop	Minimum expression proportion for the ligands/receptors (and their subunits) in the corresponding cell identities. Set to ‘0’, to return unfiltered results.	double, default: 0.1
--min_cells	Minimum cells per cell identity (‘groupby’) to be considered for downstream analysis.	integer, default: 5
--aggregate_method	Method aggregation approach, one of [‘mean’, ‘rra’], where ‘mean’ represents the mean rank, while ‘rra’ is the RobustRankAggregate (Kolde et al., 2014) of the interactions.	string, default: "rra"
--return_all_lrs	Bool whether to return all LRs, or only those that surpass the ‘expr_prop’ threshold. Those interactions that do not pass the ‘expr_prop’ threshold will be assigned to the worst score of the ones that do. ‘False’ by default.	boolean, default: FALSE
--n_perms	Number of permutations for the permutation test. Note that this is relevant only for permutation-based methods - e.g. ’CellPhoneDB	integer, default: 100

Authors

• Mauro Saporita (author)

• Povilas Gibas (author)