scverse / scanpy
Single-cell analysis in Python. Scales to >100M cells.
scverse / scanpy
scverse / gget
🧬 gget enables efficient querying of genomic reference databases
scverse / anndata
Annotated data.
scverse / PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
scverse / squidpy
Spatial Single Cell Analysis in Python
merenlab / anvio
An analysis and visualization platform for 'omics data
QING1105 / ezST
10x Visium spatial transcriptomics analysis skills for Codex — staged workflow with human review gates and LLM biological interpretation.
HERRY423 / BioNexus
Scientific reliability layer for AI-assisted biology: evaluates what evidence warrants, caps unsupported claims, audits analytical validity, and prevents silent scientific overreach.