interpret/lianapy

Description

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

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" ]  
de_method: [ "t-test" ]  
resource_name: [ "consensus" ]  
gene_symbol: [ "gene_symbol" ]  
expr_prop: [ 0.1 ]  
min_cells: [ 5 ]  
aggregate_method: [ "rra" ]  
return_all_lrs: [ false ]  
n_perms: [ 100 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.1 \  
  -main-script target/nextflow/interpret/lianapy/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input h5mu file
--output -o	file required output	Output h5mu file.
--modality	string	Which modality from the input MuData file to process.
--layer	string	Layer in anndata.AnnData.layers to use. If None, use mudata.mod[modality].X.
--de_method	string	Differential expression method. `scanpy.tl.rank_genes_groups` is used to rank genes according to 1vsRest.
--groupby	string required	The key of the observations grouping to consider.
--resource_name	string	Name of the resource to be loaded and use for ligand-receptor inference.
--gene_symbol	string	Column name in var DataFrame in which gene symbol are stored.
--expr_prop	double	Minimum expression proportion for the ligands/receptors (and their subunits) in the corresponding cell identities. Set to '0', to return unfiltered results.
--min_cells	integer	Minimum cells per cell identity ('groupby') to be considered for downstream analysis.
--aggregate_method	string	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.
--consensus_opts	string multiple	Strategies to aggregate interactions across methods. Default is None - i.e. ['Specificity', 'Magnitude'] and both specificity and magnitude are aggregated.
--return_all_lrs	boolean	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.
--n_perms	integer	Number of permutations for the permutation test. Note that this is relevant only for permutation-based methods - e.g. 'CellPhoneDB
--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

-i

file

required

--output

-o

file

required

output

--modality

string

--layer

string

--de_method

string

--groupby

string

required

--resource_name

string

--gene_symbol

string

--expr_prop

double

--min_cells

integer

--aggregate_method

string

--consensus_opts

string

multiple

--return_all_lrs

boolean

--n_perms

integer

--output_compression

string