pertdb.GeneticPerturbation .md

class pertdb.GeneticPerturbation(*args, **kwargs)

Bases: BioRecord, TracksRun, TracksUpdates

Models genetic perturbations such as CRISPR.

Parameters:

  • name – The name of the genetic perturbation.

  • system – The GeneticPerturbationSystem used to apply the genetic perturbation. Must be one of ‘CRISPR Cas9’, ‘CRISPRi’, ‘CRISPRa’, ‘shRNA’, ‘siRNA’, ‘transgene’, ‘transient transfection’.

  • on_target_score – The on-target score, indicating the likelihood of the guide RNA successfully targeting the intended DNA sequence.

  • off_target_score – The off-target score, indicating the likelihood of the guide RNA targeting unintended DNA sequences.

Example:

import pertdb

sicke_cell_perturbation = pertdb.GeneticPerturbation(
    system="CRISPR Cas9",
    name="Hemoglobin Sickle Cell Perturbation",
    sequence="AGCTGACCGTGA",
    on_target_score=85,
    off_target_score=15
).save()
name: str

Name of the Genetic perturbation.

type: GeneticPerturbationSystem

GeneticPerturbationSystem used for the genetic perturbation.

sequence: str | None

Sequence of the perturbation.

on_target_score: float | None

On-target score, indicating the likelihood of the guide RNA successfully targeting the intended DNA sequence.

off_target_score: float | None

The off-target score, indicating the likelihood of the guide RNA targeting unintended DNA sequences..

targets: PerturbationTarget

Targets of the perturbation.

artifacts: Artifact

Artifacts linked to the perturbation.