Dataset Preview
The full dataset viewer is not available (click to read why). Only showing a preview of the rows.
The dataset generation failed
Error code: DatasetGenerationError
Exception: UnicodeDecodeError
Message: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1827, in _prepare_split_single
for key, table in generator:
^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 613, in wrapped
for item in generator(*args, **kwargs):
~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/text/text.py", line 98, in _generate_tables
batch = f.read(self.config.chunksize)
File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 844, in read_with_retries
out = read(*args, **kwargs)
File "<frozen codecs>", line 325, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte
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/parquet_and_info.py", line 1369, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
~~~~~~~~~~~~~~~~~~~~~~~~~^
builder, max_dataset_size_bytes=max_dataset_size_bytes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1694, in _prepare_split
for job_id, done, content in self._prepare_split_single(
~~~~~~~~~~~~~~~~~~~~~~~~~~^
gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
):
^
File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1880, in _prepare_split_single
raise DatasetGenerationError("An error occurred while generating the dataset") from e
datasets.exceptions.DatasetGenerationError: An error occurred while generating the datasetNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
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TCGA
A multi-omics subset of the TCGA PanCancer Atlas (RNA, methylation, mutation, clinical), for use with AUTOENCODIX tutorials.
Base set (for Vanillix and other Tutorials)
Covers 8 cancer types: BRCA, OV, LUAD, UCEC, LUSC, COAD, READ, UCS.
rna.parquet— 3552 samples × 17448 genes (RNA expression)methylation.parquet— 3875 samples × 9829 genes (per-gene methylation)mutation.parquet— 3461 samples × 20304 genes (combined mutation/CNA score per gene; restricted to samples that belong to the 8 cancer types above — the source file is a pan-cancer TCGA mutation matrix, trimmed here to match this cohort)clinical.parquet— 3902 samples × 56 columns (sample-level clinical/annotation metadata, incl.CANCER_TYPE_ACRONYM,SUBTYPE)
Gene identifiers are NCBI/Entrez gene IDs throughout, consistent with the ontology files below.
ontology/ — extension for Ontix Tutorial
Two ontology hierarchies, each as a 2-level gene-grouping file (gene ID → level-1 group, level-1 group → level-2 group):
chromosome_ont_lvl1_ncbi.txt,chromosome_ont_lvl2.txt— chromosome/cytoband-based groupingreactome_ont_lvl1.txt,reactome_ont_lvl2.txt— Reactome pathway-based grouping (level 2 uses human-readable Reactome pathway names)
xmodalix/ — extension for XModalix Tutorial
Synthetic MNIST-style images paired to TCGA samples, one per sample, for the image↔omics translation tutorial:
xmodalix/tcga_fake_images.zip— 3907 grayscale 28×28 PNGsxmodalix/tcga_image_mappings.txt— tab-separatedsample_ids,img_paths,extra_class_labels,CANCER_TYPE_ACRONYM; 3230 of the 3902 base-set clinical samples have a paired image (one image label per cancer type)
Loading
from huggingface_hub import hf_hub_download
import pandas as pd
rna_path = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="rna.parquet")
meth_path = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="methylation.parquet")
mut_path = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="mutation.parquet")
clin_path = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="clinical.parquet")
rna = pd.read_parquet(rna_path)
Ontix additionally needs, e.g.:
chr1 = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="ontology/chromosome_ont_lvl1_ncbi.txt")
rea1 = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="ontology/reactome_ont_lvl1.txt")
XModalix additionally needs:
images_zip = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="xmodalix/tcga_fake_images.zip")
mapping = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="xmodalix/tcga_image_mappings.txt")
License
CC0 1.0 (Public Domain Dedication). The TCGA PanCancer Atlas open-access data
(RNA, methylation, mutation, clinical) is designated public domain by the NIH Genomic
Data Commons, with no restrictions on reuse. The Reactome pathway groupings in
ontology/ are separately licensed under CC0 by Reactome. The synthetic xmodalix/
images are generated by this project and released under the same CC0 terms.
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