datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
tcga-brca-titan-idc-ilc
tcga-brca-titan-idc-ilc
1. Tổng quan
[CẦN ĐIỀN THỦ CÔNG: mục đích, ngữ cảnh tạo dataset]
Tổng số bản ghi (cộng tất cả manifest phát hiện được): 4228
Số manifest phát hiện được trong bộ nhớ: 3 (df, brca_df, full_df)
Repo HuggingFace: okbro1234/tcga-brca-titan-idc-ilc
2. Cấu trúc lưu trữ tại đích
/ # suy từ hàm `HfApi`
file.txt # suy từ hàm `HfApi`
lfs.bin # suy từ hàm `HfApi`
shard_{i}_of_5.bin # suy từ hàm `HfApi`
remote/file/path.h5 #… See the full description on the dataset page: https://huggingface.co/datasets/okbro1234/tcga-brca-titan-idc-ilc.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_OncoTree_pt2
TCGA_OncoTree_pt2
1. Tổng quan
[CẦN ĐIỀN THỦ CÔNG: mục đích, ngữ cảnh tạo dataset]
Tổng số bản ghi (cộng tất cả manifest phát hiện được): 23984
Số manifest phát hiện được trong bộ nhớ: 3 (df, labels_df, progress)
Repo HuggingFace chính: ento3686/TCGA_OncoTree_pt2
⚠️ Dataset được lưu trên 2 repo/tài khoản HuggingFace khác nhau:
ento3686/TCGA_OncoTree_pt2 (biến: REPO_ID_2, UPLOAD_REPO_ID, CENTRAL_PROGRESS_REPO_ID, _repo_id_var)
tuna2004/TCGA_OncoTree (biến:… See the full description on the dataset page: https://huggingface.co/datasets/ento3686/TCGA_OncoTree_pt2.TCGA_virtual_spatial_transcriptomics_atlas
TCGA virtual spatial transcriptomics atlas
This repository contains predicted spatial transcriptomics for TCGA H&E slides,
both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE), produced
with DeepSpot-M.
Authors: Kalin Nonchev, Sebastian Dawo, Karina Silina, Viktor Hendrik
Koelzer, and Gunnar Rätsch.
Model: ratschlab/DeepSpotM · Code: github.com/ratschlab/DeepSpotM · Paper: medRxiv 2026.06.19.26356060.
News
[09.2026] Introducing Aurora - a no-code… See the full description on the dataset page: https://huggingface.co/datasets/ratschlab/TCGA_virtual_spatial_transcriptomics_atlas.tcga-ut
Histology images from uniform tumor regions in TCGA Whole Slide Images (TCGA-UT-Internal, TCGA-UT-External)
This repository provides a benchmarking framework for the TCGA histology image dataset originally published on Zenodo. It includes predefined train/validation/test splits and example code for foundation model evaluation.
Task
Classification of 31 different cancer types from tumor histopathological images.
Original Dataset Description… See the full description on the dataset page: https://huggingface.co/datasets/dakomura/tcga-ut.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.Refined-TCGA-PRAD-Prostate-Cancer-Pathology-Dataset
Note: Our 245 TCGA cases are ones we identified as having potential for improvement.
We plan to upload them in two phases: the first batch of 138 cases, and the second batch of 107 cases in the quality review pipeline, we plan to upload them around early of January, 2025.
Dataset: A Second Opinion on TCGA PRAD Prostate Dataset Labels with ROI-Level Annotations
Overview
This dataset provides enhanced Gleason grading annotations for the TCGA PRAD prostate cancer… See the full description on the dataset page: https://huggingface.co/datasets/Humanbased-AI/Refined-TCGA-PRAD-Prostate-Cancer-Pathology-Dataset.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.TCGAtcga-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-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-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-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-tissue-segmentation
Overview
This dataset consists of 242 images from The Cancer Genome Atlas (TCGA) pathology dataset manually annotated for segmentation of tissue (i.e. pixel-level annotation of presence or absence of tissue).
Each image is a full TCGA slide (mostly H&E) downsampled to 10 microns per pixel (MPP) and saved as a PNG.
Each image has a corresponding mask, which is also saved as a PNG where each pixel corresponds to the pixel at the same position in the 10 MPP image.
The pixel values of… See the full description on the dataset page: https://huggingface.co/datasets/conflux-xyz/tcga-tissue-segmentation.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.