config.vsh.yaml

__merge__: ../../api/comp_method.yaml
name: scbsp
label: scBSP
summary: scBSP identifies spatially variable genes via granularity-based spatial statistics.
description: |
  scBSP (single-cell BinSpect) detects spatially variable genes using a
  granularity-based approach that tests for spatial patterns at multiple
  resolutions. It bins spatial coordinates into grids at different
  granularity levels and tests whether gene expression shows significant
  spatial structure using a permutation-based statistical test. The method
  is designed for large-scale spatial transcriptomics data.
references:
  bibtex:
    - |
      @article{li2024scbsp,
        title={scBSP: A fast and accurate tool for identifying spatially variable
               genes from spatial transcriptomic data},
        author={Li, Jinpu and Shang, Yiqing and others},
        journal={Bioinformatics},
        year={2024}
      }
info:
  preferred_normalization: counts
links:
  repository: https://github.com/juexinwang/scBSP
resources:
  - type: python_script
    path: script.py
engines:
  - type: docker
    image: openproblems/base_python:1.0.0
    setup:
      - type: python
        packages:
          - pandas
          - numpy
          - scipy
          - anndata
          - scbsp
runners:
  - type: executable
  - type: nextflow
    directives:
      label: [midtime, highmem, lowcpu]