| # Cellxgene Human Aging Meta Summary | |
| A curated summary of human single-cell RNA-seq datasets from [cellxgene](https://cellxgene.cziscience.com/), focused on aging and development, with standardized metadata across experiments and assays. | |
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| ## Intended Use | |
| This summary is intended as a scaffold for integrating other curated or custom single-cell datasets (e.g., aging or disease-focused studies) with Cellxgene metadata. Enables exploration, QC, and pre-integration filtering at the experiment level. The `seafront` package contains code to pull the gene matrices associated with this metadata. | |
| ## Dataset Description | |
| This dataset provides a summarized table where: | |
| - Each row corresponds to a unique `dataset_id` + simplified assay combination (`experiment`). | |
| - Numeric columns (e.g. `n_measured_vars`, `raw_sum`) are aggregated as **medians** per dataset. | |
| - Categorical metadata (e.g. `cell_type`, `assay`, `tissue`, `disease`) are reported as **comma-separated unique values**. | |
| - Ontology term IDs are also preserved and listed uniquely. | |
| - Ambiguous developmental stages are filtered out; valid stages are converted to integer ages (`age_int`). | |
| - Low-quality experiments (e.g. with median counts < 3000) are excluded. | |
| ## Data Sources | |
| - Data pulled from the `cellxgene_census` API (version 2025-01) using `cellxgene_census.open_soma()`. | |
| - All human single-cell datasets with interpretable metadata and sufficient quality metrics were included. | |
| ## Processing Steps | |
| - **Assay Simplification**: Assay names are normalized into categories like `10x_3_prime`, `10x_5_prime`, `BD_WTA`, `ScaleBio`, etc. | |
| - **Experiment Definition**: An `experiment` is defined as a unique combination of `dataset_id` and `assay_simple`. | |
| - **Age Filtering**: Text-based developmental stages are mapped to integer age values using a rule-based filter. | |
| - **Quality Filtering**: Datasets with median raw counts < 3000 are excluded. | |
| - **Metadata Summary**: Output table generated using a per-experiment groupby summarization of all relevant columns. | |
| ## Files | |
| - `cellxgene_human_dataset_overview.parquet`: Cleaned and summarized metadata per experiment. | |
| - All variable names used in the datasets are saved for future integration compatibility. | |
| ## Example Columns | |
| - `experiment`, `dataset_id`, `donor_id` | |
| - `unique_cell_types_present` | |
| - `unique_tissues_present` | |
| - `unique_assays_present`, `assay_simple` | |
| - `median_raw_sum`, `median_n_measured_vars` | |
| - `age_int` (if available) | |
| ## Citation | |
| Please cite the original Cellxgene datasets as per their respective DOIs. This metadata summary is derived and standardized but does not modify raw gene expression data. | |