Pseudotime Root Selector

Select the earliest cell as the pseudotime trajectory root.

Description

A supplied pseudotime ordering has an earliest numeric value.

A supplied pseudotime ordering has an earliest numeric value. Picking that cell as a root is a bookkeeping operation distinct from establishing biological direction.^[1]

Select the earliest cell as the pseudotime trajectory root.

When to use Pseudotime Root Selector

Use this tool to select the earliest cell as the pseudotime trajectory root.

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 Pseudotime Root 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 cellIds, pseudotimes using the field table and calculation rules, then run the tool.
Read rootCellId, rootIndex, maximumPseudotime. 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
pseudotimes	Pseudotimes	list of number	Required

Enter aligned nonempty cell IDs and finite pseudotimes. Return the ID at the first minimum, its zero-based index and maximum pseudotime. Signed pseudotimes and repeated IDs are accepted; equal minimum values choose the first.

rootIndex=first index of minimum supplied pseudotime

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

Output field	Meaning	Value type
rootCellId	Root cell id	string
rootIndex	Root index	number
maximumPseudotime	Maximum pseudotime	number

json

{
  "input": {
    "cellIds": [
      "a",
      "b",
      "c"
    ],
    "pseudotimes": [
      0.5,
      0.1,
      0.9
    ]
  },
  "output": {
    "rootCellId": "b",
    "rootIndex": 1,
    "maximumPseudotime": 0.9
  }
}

Limitations and assumptions

No trajectory, root orientation or latent time is inferred. This assumes upstream pseudotime values already use the intended ordering and are comparable.

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 RNA Velocity Ratio: Summarize spliced-to-unspliced ratios without claiming inferred latent time. For a complementary task, use Branch Divergence: Measure trajectory branch divergence from aligned expression profiles.

References

Pseudotime Root Selector — tool.io

Similar or alternative tools

RNA Velocity Ratio
Summarize spliced-to-unspliced ratios without claiming inferred latent time.
Branch Divergence
Measure trajectory branch divergence from aligned expression profiles.