sc-batch-integration

name	sc-batch-integration
description	Integrate multi-sample scRNA-seq data with Harmony, scVI, scANVI, BBKNN, Scanorama, or supported R-backed integration methods.
version	0.5.0
author	OmicsClaw
license	MIT
tags	["singlecell","batch-integration","harmony","scvi","scanorama","bbknn"]
metadata	{"omicsclaw":{"domain":"singlecell","allowed_extra_flags":["--batch-key","--method","--n-epochs","--no-gpu","--n-latent","--labels-key","--harmony-theta","--bbknn-neighbors-within-batch","--scanorama-knn","--integration-features","--integration-pcs","--simba-n-top-genes","--simba-n-components","--simba-k","--simba-num-workers","--r-enhanced"],"param_hints":{"harmony":"[Truncated]","scvi":"[Truncated]","scanvi":"[Truncated]","bbknn":"[Truncated]","scanorama":"[Truncated]","fastmnn":"[Truncated]","seurat_cca":"[Truncated]","seurat_rpca":"[Truncated]"},"legacy_aliases":["sc-integrate"],"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":["batch integration","batch effect","harmony","scvi","bbknn","merge samples"]}}

Single-Cell Batch Integration

Why This Exists

• Without it: technical batch structure dominates embeddings and cluster separation.
• With it: integrated representations make cross-sample comparison easier.
• Why OmicsClaw: one contract standardizes multiple integration backends and their diagnostics.

Core Capabilities

1. Multiple integration backends: Harmony, scVI, scANVI, BBKNN, Scanorama, plus supported R-backed methods.
2. Shared batch contract: one batch_key-centric interface across Python and R paths.
3. Standard integration gallery: batch-colored UMAP plus label-aware diagnostics when stable labels already exist.
4. Figure-ready exports: figure_data/ CSVs plus a gallery manifest for downstream restyling.
5. Downstream-ready export: writes integrated processed.h5ad, tables, report, structured result JSON, README, and notebook bundle.

Scope Boundary

Actively implemented methods in this wrapper:

1. harmony
2. scvi
3. scanvi
4. bbknn
5. scanorama

Graph-embedding methods (require additional packages):

1. simba — SIMBA graph-embedding integration via PBG (requires simba package)

R-backed methods (require corresponding R packages):

1. fastmnn
2. seurat_cca
3. seurat_rpca

Input Formats

Format	Extension / form	Current wrapper support	Notes
AnnData	.h5ad	yes	current direct input path
Demo	--demo	yes	bundled merged-example fallback

Input Expectations

• Required metadata: a batch column such as batch, sample, or sample_id.
• Expected state: normalized data plus PCA or data suitable for PCA recomputation.