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meta.yaml
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meta.yaml
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name: immunedeconv
description: |
Perform immune deconvolution from human or mouse gene expression with immunedeconv
url: https://github.com/omnideconv/immunedeconv/tree/master
authors:
- Thibault Dayris
input:
- expr: Path to gene expression matrix (RDS, CSV, or TSV formatted).
- signature: Optional path to custom cell-type signatures.
- cibersort_bin: Path to CIBERSORT binary, required for CIBERSORT deconvolution.
- cibersort_mat: Path to CIBERSORT signatures matrix, required for CIBERSORT deconvolution.
output:
- Path to deconvolution result (RDS, CSV, or TSV formatted).
params:
- method: Optional immunedeconv method to use, default = "deconvolute"
- extra: Optional parameters to provide to immunedeconv, besides `gene_expression_matrix`, and `signature_matrix`.
note: |
* Input and output matrices cas be either `RDS`, `csv` or `tsv` formatted.
* Since CIBERSORT is not available through `conda`, binary must be provided.
* Warning: The `method` parameter is case sensitive.