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SCANPY

Definition
AI-generated

SCANPY is a Python library for analysis of large single-cell gene expression datasets, covering preprocessing, normalization, visualization (e.g. on embeddings), clustering, and marker discovery in a workflow often paired with AnnData objects.

Topics
Single-cell analysis
URL
https://scanpy.readthedocs.io/
Related
Python pandas Principal Component Analysis (PCA)

Why it matters in GWAS

Many published scRNA-seq and sc-eQTL pipelines use SCANPY-compatible steps; understanding this stack helps reproduce atlases and pseudobulk inputs that feed GWAS integration.

Example usage

"We followed a standard SCANPY workflow through normalization, highly variable gene selection, and neighborhood graph clustering."

Python pandas Principal Component Analysis (PCA) RNA Sequencing (RNA-seq) Single-Cell Sequencing UMAP
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Wolf FA, Angerer P, Theis FJ. (2018). SCANPY: large-scale single-cell gene expression data analysis. Genome Biol.
  • Cuomo ASE, Nathan A, Raychaudhuri S, et al. (2023). Single-cell genomics meets human genetics. Nat Rev Genet. https://doi.org/10.1038/s41576-023-00599-5
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