datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
TCGA-12K-parquet
TCGA-12K Parquet
Attribution
This dataset contains 224 x 224 JPEG patches from whole-slide images originally downloaded from The Cancer Genome Atlas (TCGA) that are available in the NCI Genomic Data Commons (GDC) Open Access tier. We mirror and repackage a commonly used ~12k WSI subset in parquet format for ease of training. We exclude patches that did not pass HSV thresholding, following the procedure in Kaiko.AI's Midnight paper. Patches were randomly sampled across… See the full description on the dataset page: https://huggingface.co/datasets/medarc/TCGA-12K-parquet.TCGA
Dataset Card for The Cancer Genome Atlas (TCGA) Multimodal Dataset
The Cancer Genome Atlas (TCGA) Multimodal Dataset is a comprehensive collection of clinical data, pathology reports, slide images, molecular data, and radiology images for cancer patients.
This dataset aims to facilitate research in multimodal machine learning for oncology by providing embeddings generated using state-of-the-art models including GatorTron, MedGemma, Qwen, Llama, UNI, SeNMo, REMEDIS, and… See the full description on the dataset page: https://huggingface.co/datasets/Lab-Rasool/TCGA.TCGA-12K-parquet-shuffled
TCGA-12K Parquet (Shuffled)
Attribution
This dataset contains 224 x 224 JPEG patches from whole-slide images originally downloaded from The Cancer Genome Atlas (TCGA) that are available in the NCI Genomic Data Commons (GDC) Open Access tier. We mirror and repackage a commonly used ~12k WSI subset in parquet format for ease of training. We exclude patches that did not pass HSV thresholding, following the procedure in Kaiko.AI's Midnight paper. Patches were randomly sampled… See the full description on the dataset page: https://huggingface.co/datasets/medarc/TCGA-12K-parquet-shuffled.tcga-tgct-tabular-open
TCGA-TGCT — Tabular (Open Access)
Open-access TCGA-TGCT data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 04:21:25 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-tgct-tabular-open.tcga-acc-tabular-open
TCGA-ACC — Tabular (Open Access)
Open-access TCGA-ACC data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 03:44:59 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-acc-tabular-open.tcga-read-tabular-open
TCGA-READ — Tabular (Open Access)
Open-access TCGA-READ data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 04:16:05 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-read-tabular-open.tcga-gene-expression-quantification-open
TCGA Gene Expression Quantification — Open Access
Every open-access TCGA RNA-Seq gene expression file from the NCI Genomic Data Commons (GDC), stacked into matrices: one row per sequenced tube of RNA, called an aliquot, and one column per gene. Every value is exactly as GDC published it.
Size: 11,505 aliquots × 60,660 genes, from 10,517 patients in 33 TCGA projects
Source: GDC Data Release 46.0 (2026-08-10)
Built: 2026-09-23 04:56:55 UTC
The source files
GDC… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-gene-expression-quantification-open.tcga-kich-tabular-open
TCGA-KICH — Tabular (Open Access)
Open-access TCGA-KICH data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 03:58:23 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-kich-tabular-open.tcga-uvm-tabular-open
TCGA-UVM — Tabular (Open Access)
Open-access TCGA-UVM data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 04:27:20 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-uvm-tabular-open.tcga-ucec-tabular-open
TCGA-UCEC — Tabular (Open Access)
Open-access TCGA-UCEC data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 04:24:58 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-ucec-tabular-open.tcga-dlbc-tabular-open
TCGA-DLBC — Tabular (Open Access)
Open-access TCGA-DLBC data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 03:53:50 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-dlbc-tabular-open.BraTS-TCGA
BraTS-TCGA (BraTS-TCGA-GBM + BraTS-TCGA-LGG)
Expert segmentation labels for the pre-operative TCGA glioma MRI cohorts
(Bakas et al. 2017), combining the two TCIA analysis-result collections
BraTS-TCGA-GBM (102 glioblastoma patients) and BraTS-TCGA-LGG
(65 lower-grade glioma patients) = 167 cases.
What this is (faithful-naming note): the publicly released training
half of the pre-operative subset of TCGA-GBM / TCGA-LGG, already
co-registered to a T1 template, resampled to 1 mm³… See the full description on the dataset page: https://huggingface.co/datasets/MedOtter/BraTS-TCGA.tcga-ucs-tabular-open
TCGA-UCS — Tabular (Open Access)
Open-access TCGA-UCS data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 04:27:02 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-ucs-tabular-open.tcga-laml-tabular-open
TCGA-LAML — Tabular (Open Access)
Open-access TCGA-LAML data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 04:02:09 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-laml-tabular-open.tcga-paad-tabular-open
TCGA-PAAD — Tabular (Open Access)
Open-access TCGA-PAAD data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 04:12:24 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-paad-tabular-open.tcga-chol-tabular-open
TCGA-CHOL — Tabular (Open Access)
Open-access TCGA-CHOL data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 03:38:00 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-chol-tabular-open.tcga-esca-tabular-open
TCGA-ESCA — Tabular (Open Access)
Open-access TCGA-ESCA data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 03:54:06 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-esca-tabular-open.tcga-pcpg-tabular-open
TCGA-PCPG — Tabular (Open Access)
Open-access TCGA-PCPG data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 04:13:13 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-pcpg-tabular-open.tcga-thym-tabular-open
TCGA-THYM — Tabular (Open Access)
Open-access TCGA-THYM data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 04:24:24 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-thym-tabular-open.tcga-meso-tabular-open
TCGA-MESO — Tabular (Open Access)
Open-access TCGA-MESO data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 04:10:59 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-meso-tabular-open.tcga-sarc-tabular-open
TCGA-SARC — Tabular (Open Access)
Open-access TCGA-SARC data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 04:16:39 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-sarc-tabular-open.tcga-coad-tabular-open
TCGA-COAD — Tabular (Open Access)
Open-access TCGA-COAD data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 03:52:16 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-coad-tabular-open.tcga-kirc-tabular-open
TCGA-KIRC — Tabular (Open Access)
Open-access TCGA-KIRC data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 03:58:45 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-kirc-tabular-open.tcga-stad-tabular-open
TCGA-STAD — Tabular (Open Access)
Open-access TCGA-STAD data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 04:19:42 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-stad-tabular-open.TCGA-LGG-Mask
TCGA-LGG-Mask — LGG Segmentation Dataset (Brain MRI)
Mirror of the LGG Segmentation Dataset ("Brain MRI segmentation"), the
canonical release by Mateusz Buda on Kaggle
(mateuszbuda/lgg-mri-segmentation), associated with:
Buda M., Saha A., Mazurowski M.A. Association of genomic subtypes of
lower-grade gliomas with shape features automatically extracted by a deep
learning algorithm. Computers in Biology and Medicine 109:218-225, 2019.
Brain MRI of 110 patients from the TCIA… See the full description on the dataset page: https://huggingface.co/datasets/MedOtter/TCGA-LGG-Mask.tcga-coad-msi-msstcga-gbm-tabular-open
TCGA-GBM — Tabular (Open Access)
Open-access TCGA-GBM data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 03:54:54 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-gbm-tabular-open.tcga-blca-tabular-open
TCGA-BLCA — Tabular (Open Access)
Open-access TCGA-BLCA data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 03:45:21 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-blca-tabular-open.tcga-cesc-tabular-open
TCGA-CESC — Tabular (Open Access)
Open-access TCGA-CESC data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 03:51:01 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-cesc-tabular-open.tcga-skcm-tabular-open
TCGA-SKCM — Tabular (Open Access)
Open-access TCGA-SKCM data from the NCI Genomic Data Commons, reshaped into one table per GDC data_type. Clinical, biospecimen and every open molecular modality for this cohort, in one place, queryable without downloading a single .tar or parsing a single TSV.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 04:17:45 UTC
Scope: one TCGA project — see [the family][repo] for the others
from datasets import load_dataset… See the full description on the dataset page: https://huggingface.co/datasets/gabrielaltay/tcga-skcm-tabular-open.