datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
TCGA-PANCAN-HiSeq-2770x20530gene expression cancer RNA-Seq - Check the original submission: - https://www.synapse.org/Synapse:syn2812925 - is maintained by the cancer genome atlas pan-cancer analysis project. - TCGA-PANCAN-HiSeq-2770x20530
Files combined:
unc.edu_BRCA_IlluminaHiSeq_RNASeqV2.geneExp (20530, 957) BRCA
unc.edu_KIRC_IlluminaHiSeq_RNASeqV2.geneExp (20530, 552) KIRC
unc.edu_LUAD_IlluminaHiSeq_RNASeqV2.geneExp (20530, 413) LUAD
unc.edu_THCA_IlluminaHiSeq_RNASeqV2.geneExp (20530, 471) THCA… See the full description on the dataset page: https://huggingface.co/datasets/Fllamber/TCGA-PANCAN-HiSeq-2770x20530.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
Cohort-wide gene expression matrices for the open-access TCGA RNA-Seq data distributed by the NCI Genomic Data Commons. GDC serves these measurements one file per aliquot; here they are arranged as one row per sample, with each quantification carried as its own matrix over identical axes.
GDC data release: Data Release 46.0 - August 10, 2026
Built: 2026-09-12 03:16:09 UTC
Shape: 11,505 samples x 60,660 genes
Projects: 33
Other… 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-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.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-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-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-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-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-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-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-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-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-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-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-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-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-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-OV-AS
The Cancer Genome Atlas Ovarian Cancer for Ascites Segmentation (TCGA-OV-AS)
This dataset was curated as part of the research 'Deep Learning Segmentation of Ascites on Abdominal CT Scans for Automatic Volume Quantification' (Paper, arXiv).
To replicate TCGA-OV-AS, please download TCGA-OV from TCIA using the Descriptive Directory Name download option.
Converting Images
Convert the DICOMs to NIFTI format using dcm2niix and GNU parallel.
Create the directory structure… See the full description on the dataset page: https://huggingface.co/datasets/farrell236/TCGA-OV-AS.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-thca-tabular-open
TCGA-THCA — Tabular (Open Access)
Open-access TCGA-THCA 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 04:22:10 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-thca-tabular-open.gene-expression-tcga-cptac-survival-analysistcga-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.tcga-lusc-tabular-open
TCGA-LUSC — Tabular (Open Access)
Open-access TCGA-LUSC 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 04:09:08 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-lusc-tabular-open.