sc-velocity

name	sc-velocity
description	Run scVelo on a velocity-ready h5ad using stochastic, dynamical, or steady-state modes. Use `sc-velocity-prep` first if spliced/unspliced layers are missing.
version	0.3.0
author	OmicsClaw
license	MIT
tags	["singlecell","velocity","scvelo","latent-time","dynamics"]
metadata	{"omicsclaw":{"domain":"singlecell","allowed_extra_flags":["--method","--mode","--n-jobs","--r-enhanced"],"param_hints":{"scvelo_stochastic":"[Truncated]","scvelo_dynamical":"[Truncated]","scvelo_steady_state":"[Truncated]"},"saves_h5ad":true,"requires_preprocessed":true,"requires":{"bins":"[Truncated]","env":"[Truncated]","config":"[Truncated]"},"emoji":"S","homepage":"https://github.com/OmicsClaw/OmicsClaw","os":["macos","linux"],"install":["[Truncated]"],"trigger_keywords":["rna velocity","velocity","scvelo","spliced unspliced","cellular dynamics","velovi","velocity pseudotime"]}}

Single-Cell Velocity

Why This Exists

• Without it: velocity analyses are hard to standardize because they require special input layers and backend-specific wording.
• With it: velocity backend selection and output naming are consistent across runs.
• Why OmicsClaw: one wrapper captures velocity figures, latent-time summaries, and method provenance.

Core Capabilities

1. Three scVelo modes: stochastic, dynamical, and steady-state.
2. Public alias compatibility: both --method and --mode map into the same backend selection logic.
3. Velocity-specific exports: stream plot, magnitude plot, and optional latent-time view.
4. Explicit layer contract: requires spliced and unspliced layers before execution.
5. Downstream-ready export: writes processed.h5ad, a compatibility alias adata_with_velocity.h5ad, report, result JSON, README, notebook artifacts, and figure-data tables.

Data / State Requirements

Requirement	Where it should exist	Why it matters
Velocity-ready layers	layers["spliced"], layers["unspliced"]	required for every scVelo mode
Raw counts source	layers["counts"] preferred	retained for downstream provenance and matrix-contract stability
Embedding / graph state	obsm["X_umap"], uns["neighbors"] preferred	improves interpretability and avoids unnecessary recomputation

Matrix expectations:

• input object: velocity-ready single-cell AnnData
• output object: processed.h5ad
• adata.X: normalized_expression
• layers["counts"]: raw counts
• adata.raw: raw-count snapshot

Scope Boundary

Implemented backends:

1. scvelo_stochastic
2. scvelo_dynamical