Single-cell Analysis / Python package
Scanpy
Move from a single-cell expression matrix to quality checks, clusters, and exploratory plots in Python.
Best fit
Analysts who want a scriptable workflow for exploring single-cell RNA sequencing data.
What you need
A Python environment and a gene-by-cell dataset represented as, or importable into, AnnData.
What to check
Cluster labels and visual separation depend on preprocessing and parameters. Check them against sample metadata and known markers.