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CLAM

mahmoodlab /CLAM

Open source tools for computational pathology - Nature BME

deep-learning tcga-data weakly-supervised-learning bioimage-informatics digital-pathology clam pathology whole-slide-imaging computational-pathology camelyon16 histopathology camelyon17 data-efficient mahmoodlab quantitative-pathology

UpdatedApr 14, 2025
Python

BioinformaticsFMRP /TCGAbiolinks

TCGAbiolinks

r tcga bioc bioconductor gdc integrative-analysis tcgabiolinks tcga-data

UpdatedOct 7, 2025
R

MarvinLer /tcga_segmentation

Whole Slide Image segmentation with weakly supervised multiple instance learning on TCGA | MICCAI2020https://arxiv.org/abs/2004.05024

tcga medical-imaging segmentation image-segmentation tcga-data weakly-supervised-learning miccai pathology whole-slide-imaging wsi computational-pathology multiple-instance-learning tumor-segmentation histopathology data-efficient slide-image-segmentation

UpdatedAug 5, 2021
Python

KatherLab /STAMP

Solid Tumor Associative Modeling in Pathology

bioinformatics research deep-learning mcp survival-analysis agents tcga-data weakly-supervised-learning digital-pathology pathology whole-slide-imaging bioimage-analysis histopathology heatmaps-visualization-tool mcp-server pathology-informatics

UpdatedDec 4, 2025
Python

PoisonAlien /TCGAmutations

R data package for pre-compiled somatic mutations from TCGA cohorts and CCLE

somatic-variants mutations maf tcga-data ccle maftools

UpdatedOct 4, 2024
R

sigven /oncoEnrichR

Explore the cancer relevance of your gene list

cancer proteins disease-gene-association tcga-data crispr-target protein-protein-interaction co-expression report-generator prioritization genesets high-throughput-screening cancer-survival functional-enrichment-analysis pathway-enrichment-analysis protein-complexes tissue-enrichment-analysis cancer-hallmark-evidence

UpdatedDec 17, 2025
R

BioinformaticsFMRP /TCGAbiolinksGUI

TCGAbiolinksGUI code development for R/Bioconductor submissionhttp://tcgabiolinks.fmrp.usp.br:3838/

gui r bioconductor gdc tcgabiolinks tcga-data integrative

UpdatedAug 2, 2021
R

rezacsedu /Multimodal-autoencoder-for-breast-cancer

Prognostically Relevant Subtypes and Survival Prediction for Breast Cancer Based on Multimodal Genomics Data

deep-learning regression neural-networks cancer-genomics classification multimodality tcga-data survival-prediction multimodal-autoencoder

UpdatedAug 13, 2019
Python

waldronlab /MultiAssayWorkshop

Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment

bioconductor tcga-data multiassayexperiment multi-omic-data u24ca289073

UpdatedJul 2, 2025
TeX

KChen-lab /Texomer

Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data

statistical-inference functional-variants tcga-data tumor-heterogeneity

UpdatedAug 19, 2020
R

mahmoodlab /CPATH_demographics

Demographic bias in misdiagnosis by computational pathology models - Nature Medicine

tcga-data fairness digital-pathology computational-pathology ai-health ai-fairness bias-fairness-metrics ai4health health-disparities ebrains demographic-bias pathology-bias ai4health-bias algorithimic-fairness pathology-disparities ai-bias-testing quantitative-pathology

UpdatedApr 29, 2024
Python

HuaZou /bioinformatics_pipeline

Bioinformatics Pipeline

rna-seq snakemake pipeline metagenomics methylation data-analysis amplicon tcga-data geo-data mirna-seq

UpdatedOct 7, 2022
R

MahShaaban /miRCancerdb

A database for microRNA-gene/protein expression correlation in cancer.

r database sqlite cancer-genomics tcga-data microrna

UpdatedNov 7, 2017
R

asmagen /SPAGEfinder

Computational approach to identify Survival associated Pairwise Gene Expression states.

survival-analysis interaction tcga-data genetic genetic-interactions

UpdatedJul 16, 2023
R

mschubert /TCGAbiolinks-downloader

GNU Make-driven workflow to download TCGA data via the TCGAbiolinks package

cancer reproducible-research rstats tcga-data

UpdatedJan 22, 2022
R

Eurus-Holmes /Tumor2Graph

Tumor2Graph: a novel Overall-Tumor-Profile-derived virtual graph deep learning for predicting tumor typing and subtyping.

cluster cnn tcga-data gcn multimodal-data gnn graph-deep-learning multimodal-graphs

UpdatedSep 2, 2021
Python

ShixiangWang /ImmuneDR

A Community Curated Immune Resource Database in R format

r database tcga-data immunotherapy immune-infiltration

UpdatedSep 24, 2019
R

deargen /DearWXpub

a neural network-based feature selection algorithm for next-generation sequencing data

cancer paper classification tcga-data wx-keras wx-ranking

UpdatedMar 27, 2020
R

thesis

mar-kan /thesis

BSc thesis: "Convolutional Neural Networks and their Application in Cancer Diagnosis based on RNA-Sequencing"

rna-seq deep-learning cancer tcga cnn gene-expression classification convolutional-neural-networks tcga-data pan-cancer cancer-classification

UpdatedMar 9, 2022
Jupyter Notebook

peterlipan /FoF

The official implementations of our BIBM'24 paper: Focus on Focus: Focus-oriented Representation Learning and Multi-view Cross-modal Alignment for Glioma Grading

tcga multimodality tcga-data glioblastoma cancer-grading glioma histopathology-images ieee-bibm pathology-images pathology-classification bibm-2024 tcga-gbm tcga-lgg

UpdatedNov 9, 2024
Python

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