Home / Skills / alterlab-cellxgene

alterlab-cellxgene

AlterLab-IEU/AlterLab-Academic-SkillsSkill

Query the CZ CELLxGENE Census (200M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnData. Use when pulling reference single-cell RNA-seq data from the largest curated public atlas, running population-scale queries, or benchmarking your data against a reference — for analyzing your own dataset use scanpy or scvi-tools. Part of the AlterLab Academic Skills suite.

ScannedSkillSource: GitHub
76 stars +3 this week Updated 21d ago License MIT Context ≈117 tokens always loaded
55popular

Why this score

Stars7/35
Usage (forks)2/15
Upkeep25/25
License15/15
Owner history6/10

This repo hosts 10 skills, so its 76 stars are split between them (about 8 each) for scoring.

Popularity score: 55/100 from public GitHub signals only. It shows how widely used and maintained this is, not how well it works. Not included yet: the fake-star check. The security scan is shown separately and doesn't change the score. How we rank

Security

Scanned Oct 20, 2026 at commit e4836c08a20d, with Cisco's open-source skill-scanner.

None of the patterns we list turned up: shell commands, network requests, reading environment variables, downloading and running code, or installing packages.

A scan lists patterns in the code. It can't prove an add-on is harmless, and it can miss things, so read what you install. How we scan

Alternatives

Nothing from another maker does quite the same job yet.