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Multi-omics integration for single-cell data. Use for integrating multiple modalities like RNA, ATAC, and protein in single-cell analysis.
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Basado en la clasificación ocupacional SOC
| name | scribble |
| domain | compbio |
| description | Multi-omics integration for single-cell data. Use for integrating multiple modalities like RNA, ATAC, and protein in single-cell analysis. |
| license | MIT license |
| metadata | {"skill-author":"Eric Yiru"} |
Scribble is a tool/package for multi-omics integration in single-cell analysis. It provides methods for integrating different modalities (gene expression, chromatin accessibility, protein) to create unified representations of cells.
This skill should be used when:
pip install scribble
# Or from GitHub
pip install git+https://github.com/username/scribble.git
import scribble
import scanpy as sc
import numpy as np
# Load multi-modal data
rna = sc.read_h5ad("rna.h5ad")
atac = sc.read_h5ad("atac.h5ad")
protein = sc.read_h5ad("protein.h5ad")
# Integration
combined = scribble.integrate(
[rna, atac, protein],
method="cca" # or "mnn", "wnn"
)
# Canonical Correlation Analysis
combined = scribble.integrate(
[rna, atac],
method="cca",
n_components=50
)
# Weighted nearest neighbors
combined = scribble.integrate(
[rna, protein],
method="wnn"
)
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