Download Resources
Below are the available datasets and analysis outputs. Each section includes a short description, a direct download link, and ready-to-copy wget/curl commands.
pbmcpedia-v20250915-slim.h5ad ~1.4 GB
Single-cell PBMC atlas with harmonized metadata and annotations; contains only the processed matrices for analysis.
Downloadwget -O pbmcpedia-v20250915-full.h5ad "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/pbmcpedia-v20250915-full.h5ad"curl -L "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/pbmcpedia-v20250915-full.h5ad" -o pbmcpedia-v20250915-full.h5adpbmcpedia-v20250925-complete.h5ad ~23.4 GB
Single-cell PBMC atlas with harmonized metadata and annotations; contains the processed and raw matrices.
Downloadwget -O pbmcpedia-v20250925-complete.h5ad "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/adata_w_raw.h5ad"curl -L "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/adata_w_raw.h5ad" -o pbmcpedia-v20250925-complete.h5adPseudobulk expression matrices (donor x cell type): counts aggregated across cells per donor/cell type on the broad and fine annotation levels. These matrices are used for downstream differential expression analysis.
pbmcpedia-v20250915-pseudobulk-broad.h5ad ~4.4 GB
Downloadwget -O pbmcpedia-v20250915-pseudobulk-broad.h5ad "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/pbmcpedia-v20250915-pseudobulk-broad.h5ad"curl -L "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/pbmcpedia-v20250915-pseudobulk-broad.h5ad" -o pbmcpedia-v20250915-pseudobulk-broad.h5adpbmcpedia-v20250915-pseudobulk-fine.h5ad ~10.2 GB
Downloadwget -O pbmcpedia-v20250915-pseudobulk-fine.h5ad "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/pbmcpedia-v20250915-pseudobulk-fine.h5ad"curl -L "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/pbmcpedia-v20250915-pseudobulk-fine.h5ad" -o pbmcpedia-v20250915-pseudobulk-fine.h5adProcessed downstream analysis outputs.
pbmcpedia-v20250915-pathways-gsea-summary.csv ~106 MB
Pathway enrichment summary across cell types/contrasts with core stats (NES/FDR, leading edge).
Downloadwget -O pbmcpedia-v20250915-pathways-gsea-summary.csv "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/pbmcpedia-v20250915-pathways-gsea-summary.csv"curl -L "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/pbmcpedia-v20250915-pathways-gsea-summary.csv" -o pbmcpedia-v20250915-pathways-gsea-summary.csvpbmcpedia-v20250915-deg-all-contrasts.csv ~251 MB
Differential gene expression results (limma on pseudobulks) comparing disease vs. control across cell types; includes effect sizes and FDR.
Downloadwget -O pbmcpedia-v20250915-deg-all-contrasts.csv "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/pbmcpedia-v20250915-deg-all-contrasts.csv"curl -L "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/pbmcpedia-v20250915-deg-all-contrasts.csv" -o pbmcpedia-v20250915-deg-all-contrasts.csvT-cell and B-cell receptor sequencing data from the PBMC atlas.
vdj_airr.parquet ~478 MB
VDJ sequencing data in AIRR format (parquet format for efficient storage and fast loading).
Downloadwget -O vdj_airr.parquet "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/vdj_airr.parquet"curl -L "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/vdj_airr.parquet" -o vdj_airr.parquetvdj_obs.csv.gz ~5.2 MB
VDJ cell metadata and annotations (compressed CSV format).
Downloadwget -O vdj_obs.csv.gz "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/vdj_obs.csv.gz"curl -L "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/vdj_obs.csv.gz" -o vdj_obs.csv.gzAntibody-derived tag (ADT) data for surface protein expression analysis.
protein_means_by_disease.csv ~15.9 KB
Mean protein expression by disease condition (CSV format).
Downloadwget -O protein_means_by_disease.csv "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/protein_means_by_disease.csv"curl -L "https://web.ccb.uni-saarland.de/downloads/pbmcpedia/protein_means_by_disease.csv" -o protein_means_by_disease.csv