Cell Gene Count Filter

Filter single cells by detected gene-count threshold.

Description

Detected-gene count filtering screens supplied per-cell complexity.

Detected-gene count filtering screens supplied per-cell complexity. Counts must already use a consistent definition of detected expression.^[1]

Filter single cells by detected gene-count threshold.

When to use Cell Gene Count Filter

Use this tool to filter single cells by detected gene-count threshold.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Cell Gene Count Filter and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter cellIds, detectedGeneCounts, minimumGenes using the field table and calculation rules, then run the tool.
Read retainedCellIds, rejectedCellIds, retainedPercent. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
cellIds	Cell ids	list of string	Required
detectedGeneCounts	Detected gene counts	list of number	Required
minimumGenes	Minimum genes	number	Required

Enter aligned nonempty IDs and nonnegative detected counts with a finite minimum. Partition IDs into retained and rejected lists, preserving order, and return retained percentage. Counts and criterion are not separately required to be integers.

retain if detectedGeneCount≥minimumGenes; retained%=100 retained/n

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
retainedCellIds	Retained cell ids	list of string
rejectedCellIds	Rejected cell ids	list of string
retainedPercent	Retained percent	number

json

{
  "input": {
    "cellIds": [
      "a",
      "b",
      "c"
    ],
    "detectedGeneCounts": [
      100,
      500,
      200
    ],
    "minimumGenes": 200
  },
  "output": {
    "retainedCellIds": [
      "b",
      "c"
    ],
    "rejectedCellIds": [
      "a"
    ],
    "retainedPercent": 66.66666666666666
  }
}

Limitations and assumptions

The tool does not calculate detected counts from an expression matrix or identify doublets and ambient RNA. The cutoff is supplied and is not an embedded cell-type recommendation.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Cell Mito Percent Filter: Gate each single cell by its mitochondrial UMI share. For a complementary task, use Marker Expression Fraction: Summarize a marker dot plot’s detection share and mean expression.

References

Cell Gene Count Filter — tool.io

Similar or alternative tools

Cell Mito Percent Filter
Gate each single cell by its mitochondrial UMI share.
Marker Expression Fraction
Summarize a marker dot plot’s detection share and mean expression.