Single-Cell & Genomics
Tools and datasets for single-cell RNA sequencing, spatial transcriptomics, and gene expression analysis.
Tools
Analysis Frameworks
Scanpy
Single-cell analysis in Python
Seurat
Single-cell analysis in R
Squidpy
Spatial transcriptomics analysis
Single-Cell Foundation Models
scGPT
Transformer model for single-cell
scFoundation
Foundation model for single-cell data
scPRINT
Cell imputation model
GenePT
GPT-based gene embeddings
Biomedical Language Models
Benchmarking
Datasets
Atlases & Repositories
Gene Expression Omnibus
Public functional genomics data
Single Cell Expression Atlas
scRNA atlas (EBI)
Single Cell Portal
Single cell RNA data (Broad)
10x Genomics Datasets
Single-cell datasets
Functional Genomics
Benchmarks
Awesome Lists
Getting Started
conda create -n singlecell python=3.10
conda activate singlecell
pip install scanpy squidpy jupyter