sc-perturb

Single-cell perturbation analysis for scRNA-seq perturbation screens using the official pertpy Mixscape workflow.

Dépôt: mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-
Dernière activité de la source: 30 avril 2026 à 21:29
Langue détectée de SKILL.md: anglais
Étoiles: 31
Forks: 8

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npx skills add https://github.com/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- --skill sc-perturb

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SKILL.md

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Parameter	Meaning
`--method`	currently `mixscape`
`--pert-key`	perturbation or guide label column in `adata.obs`
`--control`	control category in the perturbation column
`--split-by`	biological replicate or condition column
`--n-neighbors`	neighbors used for perturbation signature
`--logfc-threshold`	DE threshold used inside Mixscape
`--pval-cutoff`	DE p-value cutoff used inside Mixscape
`--perturbation-type`	expected perturbation label such as `KO`

Flag	Type	Default	Description	Validation
`--input`	str	None	Input AnnData file (`.h5ad`)	Required unless `--demo`
`--output`	str	—	Output directory	Required
`--demo`	flag	off	Run with built-in demo data	—
`--method`	str	`mixscape`	Analysis method (currently only `mixscape`)	Choices: `mixscape`
`--pert-key`	str	`perturbation`	`adata.obs` column containing perturbation labels	Column must exist; perturbation + control values must be present
`--control`	str	`NT`	Control label value inside the `--pert-key` column	Must match a category in `adata.obs[pert_key]`
`--split-by`	str	`replicate`	`adata.obs` column for replicate/batch splitting	Optional
`--n-neighbors`	int	20	Neighbors used for perturbation signature computation	—
`--logfc-threshold`	float	0.25	Log fold-change threshold used inside Mixscape DE	—
`--pval-cutoff`	float	0.05	P-value cutoff used inside Mixscape DE	—
`--perturbation-type`	str	`KO`	Expected perturbation class label (e.g., `KO`, `overexpression`)	—
`--seed`	int	0	Random seed for reproducibility	—
`--r-enhanced`	flag	off	Generate R Enhanced plots (requires R + ggplot2)	—

Renderer	Output file	Description
`plot_embedding_discrete`	`figures/r_enhanced/r_embedding_discrete.png`	UMAP colored by Mixscape class assignment
`plot_embedding_feature`	`figures/r_enhanced/r_embedding_feature.png`	UMAP colored by perturbation score

# Typical real-data run
python omicsclaw.py run sc-perturb \
  --input perturb_prep_output/processed.h5ad \
  --pert-key perturbation \
  --control NT \
  --output results/

# If the column names differ from defaults
python omicsclaw.py run sc-perturb \
  --input data.h5ad \
  --pert-key guide_target \
  --control non-targeting \
  --output results/

name	sc-perturb
description	Single-cell perturbation analysis for scRNA-seq perturbation screens using the official pertpy Mixscape workflow.
version	0.1.0
author	OmicsClaw
license	MIT
tags	["singlecell","perturbation","perturb-seq","crispr","mixscape","pertpy"]
metadata	{"omicsclaw":{"domain":"singlecell","allowed_extra_flags":["--method","--pert-key","--control","--split-by","--n-neighbors","--logfc-threshold","--pval-cutoff","--perturbation-type","--r-enhanced"],"saves_h5ad":true}}

name	sc-perturb
description	Single-cell perturbation analysis for scRNA-seq perturbation screens using the official pertpy Mixscape workflow.
version	0.1.0
author	OmicsClaw
license	MIT
tags	["singlecell","perturbation","perturb-seq","crispr","mixscape","pertpy"]
metadata	{"omicsclaw":{"domain":"singlecell","allowed_extra_flags":["--method","--pert-key","--control","--split-by","--n-neighbors","--logfc-threshold","--pval-cutoff","--perturbation-type","--r-enhanced"],"saves_h5ad":true}}

sc-perturb

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Single-Cell Perturbation

Why This Exists

Single-Cell Perturbation

Why This Exists

Current Methods

Key Inputs

Public Parameters

Notes

Data / State Requirements

Upstream Step

Workflow

Outputs

CLI Parameters

R Enhanced Plots

Special Requirements

Perturbation Labels in `adata.obs`

Workflow Position

sc-perturb

Informations de source

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Plus depuis ce dépôt

Plus depuis ce dépôt

Single-Cell Perturbation

Why This Exists

Single-Cell Perturbation

Why This Exists

Current Methods

Key Inputs

Public Parameters

Notes

Data / State Requirements

Upstream Step

Workflow

Outputs

CLI Parameters

R Enhanced Plots

Special Requirements

Perturbation Labels in adata.obs

Workflow Position

Perturbation Labels in `adata.obs`