seandavi / awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
seandavi / awesome-single-cell
scverse / scanpy
Single-cell analysis in Python. Scales to >100M cells.
scverse / gget
🧬 gget enables efficient querying of genomic reference databases
chanzuckerberg / cellxgene
An interactive explorer for single-cell transcriptomics data
scverse / anndata
Annotated data.
scverse / PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
jinworks / CellChat
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
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.
wrab12 / awesome-spatial-transcriptomics
A curated list of tools, foundation models, datasets and tutorials for spatial transcriptomics and single-cell analysis, ordered the way an analysis goes.
HERRY423 / BioNexus
Scientific reliability layer for AI-assisted biology: evaluates what evidence warrants, caps unsupported claims, audits analytical validity, and prevents silent scientific overreach.