sc-pseudotime

Single-cell pseudotime and lineage inference after clustering, with DPT, Palantir, VIA, CellRank, or Slingshot plus post-hoc trajectory gene ranking.

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Repository: mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-
Letzte Quellaktivität: 30. April 2026 um 21:29
Erkannte Sprache von SKILL.md: Englisch
Sterne: 31
Forks: 8

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

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SKILL.md

Quellanweisungen · Schreibgeschützte Vorschau

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name	sc-pseudotime
description	Single-cell pseudotime and lineage inference after clustering, with DPT, Palantir, VIA, CellRank, or Slingshot plus post-hoc trajectory gene ranking.
version	0.5.0
author	OmicsClaw
license	MIT
tags	["singlecell","pseudotime","trajectory","dpt","palantir","via","cellrank","slingshot"]
metadata	{"omicsclaw":{"domain":"singlecell","allowed_extra_flags":["--method","--cluster-key","--use-rep","--root-cluster","--root-cell","--end-clusters","--n-neighbors","--n-pcs","--n-dcs","--n-genes","--corr-method","--palantir-knn","--palantir-n-components","--palantir-num-waypoints","--palantir-max-iterations","--palantir-seed","--via-knn","--via-seed","--cellrank-n-states","--cellrank-schur-components","--cellrank-frac-to-keep","--cellrank-use-velocity","--r-enhanced"],"param_hints":{"dpt":"[Truncated]","palantir":"[Truncated]","via":"[Truncated]","cellrank":"[Truncated]","slingshot_r":"[Truncated]","monocle3_r":"[Truncated]"},"saves_h5ad":true,"requires_preprocessed":true,"trigger_keywords":["pseudotime","trajectory","lineage","diffusion pseudotime","palantir","via","cellrank","monocle3","slingshot"]}}

Method	Best first use	What it adds
`dpt`	most users’ first trajectory pass	classic diffusion pseudotime after graph construction
`palantir`	when entropy / fate probabilities are important	waypoint-based pseudotime and terminal-state probabilities
`via`	when users want graph-based terminal-state discovery	fast graph trajectory with branch-aware outputs
`cellrank`	when users explicitly want macrostates or fate inference	transition-kernel / fate model on top of a graph
`slingshot_r`	when users want explicit branch curves	lineage-centric branch inference through the R bridge
`monocle3_r`	when users want principal graph trajectory with branching	Monocle3 principal graph trajectory and pseudotime via R bridge. Produces monocle3_pseudotime in obs and MST trajectory edges. Requires monocle3 R package.

Flag	Type	Default	Description	Validation
`--input`	str	—	Input `.h5ad` file	required unless `--demo`
`--output`	str	—	Output directory	required
`--demo`	flag	off	Run with bundled PBMC3k data	—
`--method`	str	`dpt`	Trajectory method: `dpt`, `palantir`, `via`, `cellrank`, `slingshot_r`, `monocle3_r`	validated against METHOD_REGISTRY
`--cluster-key`	str	`leiden`	Cluster/label column in `obs`	—
`--use-rep`	str	None	Embedding to use (e.g., `X_pca`, `X_harmony`)	auto-detected when omitted
`--root-cluster`	str	None	Cluster name to use as trajectory root	—
`--root-cell`	str	None	Specific cell (obs_name or integer index) to use as root	—
`--end-clusters`	str	None	Comma-separated terminal cluster names	slingshot_r only
`--n-neighbors`	int	15	KNN size for graph construction	dpt only
`--n-pcs`	int	50	PCs to use for diffusion map	dpt only
`--n-dcs`	int	10	Number of diffusion components	dpt only
`--n-genes`

Renderer	Output file	figure_data CSV	Plot description	Required R packages
`plot_pseudotime_lineage`	`r_pseudotime_lineage.png`	`pseudotime_points.csv`	Pseudotime lineage scatter with loess trajectory curves	ggplot2
`plot_pseudotime_dynamic`	`r_pseudotime_dynamic.png`	`trajectory_genes.csv`	Dynamic gene expression trends along pseudotime	ggplot2
`plot_pseudotime_heatmap`	`r_pseudotime_heatmap.png`	`gene_expression.csv`	Heatmap of top trajectory genes ordered by pseudotime	ggplot2, ComplexHeatmap
`plot_embedding_discrete`	`r_embedding_discrete.png`	`embedding_points.csv`	UMAP/embedding colored by cluster labels	ggplot2
`plot_embedding_feature`	`r_embedding_feature.png`	`embedding_points.csv`	UMAP/embedding colored by pseudotime score	ggplot2
`plot_cell_density`	`r_cell_density.png`	`embedding_points.csv`	2D density overlay on embedding	ggplot2, ggdensity

sc-pseudotime

Installationsoptionen

Quelldateien prüfen

Single-Cell Pseudotime

What This Skill Does

What Should Usually Come Before It

Matrix / State Requirements

Public Methods

Beginner-Friendly Method Summary

Key Parameters

Always important

Method-specific

Usage Examples

Workflow

Output Contract

Usual Next Steps

Current Guardrails

CLI Parameters

R Enhanced Plots

Workflow Position

sc-pseudotime

Quellinformationen

Installationsoptionen

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Mehr aus diesem Repository

Mehr aus diesem Repository

Single-Cell Pseudotime

What This Skill Does

What Should Usually Come Before It

Matrix / State Requirements

Public Methods

Beginner-Friendly Method Summary

Key Parameters

Always important

Method-specific

Usage Examples

Workflow

Output Contract

Usual Next Steps

Current Guardrails

CLI Parameters

R Enhanced Plots

Workflow Position