HVG Dispersion Selector

Select highly variable genes by variance-to-mean dispersion.

Description

Variance-to-mean dispersion ranks genes by relative variability.

Variance-to-mean dispersion ranks genes by relative variability. Raw dispersion can depend strongly on mean expression and is distinct from a mean-adjusted HVG statistic.^[1]

Select highly variable genes by variance-to-mean dispersion.

When to use HVG Dispersion Selector

Use this tool to select highly variable genes by variance-to-mean dispersion.

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 HVG Dispersion Selector 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 geneIds, meanExpressions, variances, topCount using the field table and calculation rules, then run the tool.
Read selectedGenes, dispersions. 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
geneIds	Gene ids	list of string	Required
meanExpressions	Mean expressions	list of number	Required
variances	Variances	list of number	Required
topCount	Top count	number	Required

Enter aligned nonempty IDs, positive means, nonnegative variances and a top count within 1 through gene count. Sort dispersions descending with original-index tie breaks and return selected IDs and their dispersions. Use an integer top count; fractional values are truncated by slicing.

dispersion_i=variance_i/mean_i; select highest dispersions

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

Output field	Meaning	Value type
selectedGenes	Selected genes	list of string
dispersions	Dispersions	list of number

json

{
  "input": {
    "geneIds": [
      "g1",
      "g2",
      "g3"
    ],
    "meanExpressions": [
      10,
      20,
      10
    ],
    "variances": [
      5,
      80,
      20
    ],
    "topCount": 2
  },
  "output": {
    "selectedGenes": [
      "g2",
      "g3"
    ],
    "dispersions": [
      4,
      2
    ]
  }
}

Limitations and assumptions

Mean/variance estimation, abundance binning and library normalization are not performed. This is a raw dispersion selection rather than a full single-cell HVG pipeline.

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 Biological Variation Coefficient: Convert negative-binomial dispersions to biological coefficients of variation. For a complementary task, use Housekeeping Cv Rank: Rank housekeeping genes by replicate coefficient of variation.

References

HVG Dispersion Selector — tool.io

Similar or alternative tools

Biological Variation Coefficient
Convert negative-binomial dispersions to biological coefficients of variation.
Housekeeping Cv Rank
Rank housekeeping genes by replicate coefficient of variation.