Dataset Viewer

The dataset viewer is not available for this subset.

Cannot get the split names for the config 'default' of the dataset.

Exception:    SplitsNotFoundError
Message:      The split names could not be parsed from the dataset config.
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/inspect.py", line 299, in get_dataset_config_info
                  for split_generator in builder._split_generators(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/packaged_modules/parquet/parquet.py", line 60, in _split_generators
                  self.info.features = datasets.Features.from_arrow_schema(pq.read_schema(f))
                File "/src/services/worker/.venv/lib/python3.9/site-packages/pyarrow/parquet/core.py", line 2325, in read_schema
                  file = ParquetFile(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/pyarrow/parquet/core.py", line 318, in __init__
                  self.reader.open(
                File "pyarrow/_parquet.pyx", line 1470, in pyarrow._parquet.ParquetReader.open
                File "pyarrow/error.pxi", line 91, in pyarrow.lib.check_status
              OSError: Couldn't deserialize thrift: TProtocolException: Exceeded size limit
              
              
              The above exception was the direct cause of the following exception:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/split_names.py", line 65, in compute_split_names_from_streaming_response
                  for split in get_dataset_split_names(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/inspect.py", line 353, in get_dataset_split_names
                  info = get_dataset_config_info(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/inspect.py", line 304, in get_dataset_config_info
                  raise SplitsNotFoundError("The split names could not be parsed from the dataset config.") from err
              datasets.inspect.SplitsNotFoundError: The split names could not be parsed from the dataset config.

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YAML Metadata Warning: empty or missing yaml metadata in repo card (https://huggingface.co/docs/hub/datasets-cards)

Cellxgene Human Aging Meta Summary

A curated summary of human single-cell RNA-seq datasets from cellxgene, focused on aging and development, with standardized metadata across experiments and assays.

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.

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