SCMCP

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filter_cells

Filter single-cell RNA sequencing data by defining minimum and maximum thresholds for gene expression counts and the number of genes expressed to isolate relevant cell populations.

Instructions

Filter cells based on counts and numbers of genes expressed.

Input Schema

Name	Required	Description
`max_counts`	No	Maximum number of counts required for a cell to pass filtering.
`max_genes`	No	Maximum number of genes expressed required for a cell to pass filtering.
`min_counts`	No	Minimum number of counts required for a cell to pass filtering.
`min_genes`	No	Minimum number of genes expressed required for a cell to pass filtering.

Input Schema (JSON Schema)

{
  "description": "Input schema for the filter_cells preprocessing tool.",
  "properties": {
    "max_counts": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Maximum number of counts required for a cell to pass filtering.",
      "title": "Max Counts"
    },
    "max_genes": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Maximum number of genes expressed required for a cell to pass filtering.",
      "title": "Max Genes"
    },
    "min_counts": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Minimum number of counts required for a cell to pass filtering.",
      "title": "Min Counts"
    },
    "min_genes": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Minimum number of genes expressed required for a cell to pass filtering.",
      "title": "Min Genes"
    }
  },
  "title": "FilterCells",
  "type": "object"
}

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