tcga-data

There are 7 repositories under tcga-data topic.

CLAM
mahmoodlab / CLAM
Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering
histopathology pathology weakly-supervised-learning whole-slide-imaging data-efficient computational-pathology mahmoodlab bioimage-informatics deep-learning tcga-data camelyon16 camelyon17 clam digital-pathology quantitative-pathology
Language:Python 909
BioinformaticsFMRP / TCGAbiolinks
TCGAbiolinks
integrative-analysis bioc r tcgabiolinks bioconductor gdc tcga tcga-data
Language:R 277
MarvinLer / tcga_segmentation
Whole Slide Image segmentation with weakly supervised multiple instance learning on TCGA | MICCAI2020 https://arxiv.org/abs/2004.05024
multiple-instance-learning image-segmentation histopathology tumor-segmentation whole-slide-imaging wsi miccai tcga slide-image-segmentation tcga-data weakly-supervised-learning pathology computational-pathology data-efficient medical-imaging segmentation
Language:Python 113
PoisonAlien / TCGAmutations
R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)
maf maftools mutations somatic-variants tcga-data
Language:R 76
sigven / oncoEnrichR
Cancer-dedicated gene set interpretation
cancer high-throughput-screening tcga-data report-generator protein-protein-interaction co-expression disease-gene-association crispr-target proteins genesets prioritization protein-complexes cancer-survival functional-enrichment-analysis tissue-enrichment-analysis pathway-enrichment-analysis cancer-hallmark-evidence
Language:R 48
BioinformaticsFMRP / TCGAbiolinksGUI
TCGAbiolinksGUI code development for R/Bioconductor submission http://tcgabiolinks.fmrp.usp.br:3838/
gdc tcgabiolinks bioconductor r integrative gui tcga-data
Language:R 35
rezacsedu / Multimodal-autoencoder-for-breast-cancer
Prognostically Relevant Subtypes and Survival Prediction for Breast Cancer Based on Multimodal Genomics Data
multimodality multimodal-autoencoder cancer-genomics tcga-data neural-networks deep-learning survival-prediction classification regression
Language:Python 23
KChen-lab / Texomer
Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data
statistical-inference tumor-heterogeneity functional-variants tcga-data
Language:R 20
waldronlab / MultiAssayWorkshop
Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment
multiassayexperiment tcga-data bioconductor multi-omic-data
Language:TeX 19
HuaZou / bioinformatics_pipeline
Bioinformatics Pipeline
snakemake data-analysis pipeline metagenomics amplicon rna-seq mirna-seq methylation tcga-data geo-data
Language:R 10
MahShaaban / miRCancerdb
A database for microRNA-gene/protein expression correlation in cancer.
r sqlite database microrna tcga-data cancer-genomics
Language:R 9
asmagen / SPAGEfinder
Computational approach to identify Survival associated Pairwise Gene Expression states.
genetic genetic-interactions interaction survival-analysis tcga-data
Language:R 8
mschubert / TCGAbiolinks-downloader
GNU Make-driven workflow to download TCGA data via the TCGAbiolinks package
cancer reproducible-research rstats tcga-data
Language:R 8
deargen / DearWXpub
a neural network-based feature selection algorithm for next-generation sequencing data
tcga-data wx-keras cancer classification wx-ranking paper
Language:R 7
Eurus-Holmes / Tumor2Graph
Tumor2Graph: a novel Overall-Tumor-Profile-derived virtual graph deep learning for predicting tumor typing and subtyping.
multimodal-graphs multimodal-data tcga-data graph-deep-learning gnn cnn gcn cluster
Language:Python 7
bcgsc / tasrkleat-TCGA-analysis-scripts
This repo stores codes for the analysis of tasrkleat results on TCGA RNA-Seq dataa
tcga tcga-data cleavage-sites alternative-polyadenylation rna-seq
Language:Jupyter Notebook 4
jingxinfu / TCGAdnloader
TCGA hg19 and hg38 data downloader.
tcga-data hg38 hg19 rna-seq cnv snv
Language:Python 4
thesis
mar-kan / thesis
BSc thesis: "Convolutional Neural Networks and their Application in Cancer Diagnosis based on RNA-Sequencing"
deep-learning convolutional-neural-networks cnn classification gene-expression rna-seq cancer cancer-classification pan-cancer tcga tcga-data
Language:Jupyter Notebook 4
ShixiangWang / ImmuneDR
A Community Curated Immune Resource Database in R format
r immune-infiltration database tcga-data immunotherapy
Language:R 4
urmi-21 / TCGA-Data-Analysis
Examples on processing and working with TCGA mutation and RNA-Seq data
tcga-data gtex cancer-data tcgabiolinks bioinformatics-analysis
Language:R 4
ropensci / cRegulome
An R package to access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer
r database datascience cancer-genomics tcga-data transcription-factors microrna rstats r-package peer-reviewed
Language:R 3
averissimo / tcga.data
Genomic data from TCGA ready to be used (organized per tissue type and in matrix form)
r tcga tcga-data data-package research
Language:R 2
aws-samples / aws-glue-athena-tcga
This repository has the code for the AWS blog post - Enabling the aggregation and query of The Cancer Genome Atlas using AWS Glue and Amazon Athena
pyspark aws-glue aws-athena r tcga-data
Language:Jupyter Notebook 2
uazadi / TIDaC
TCGA and TCIA Images Dataset Creator
tcga-data tcia medical-imaging tcga r cancer rest-api
Language:R 2
WPZgithub / ConMod
Identifying conserved functional modules in multiple biological networks
multi-view-clustering non-negative-matrix-factorization tcga-data
Language:MATLAB 2
adrian-aleks / TCGA-clasterization
Clasterization of TCGA dataset. Data preprocessing, visualization and clasterization with different alghoritms. Done mostly with Python 3.7 and Scikit-Learn library.
clasterization unsupervised-learning python tcga-data
Language:Jupyter Notebook 1
Akenaide / wsoffcli
POC ws-tcg scrapper
go tcga-data scraper cli weiss weiss-schwarz
Language:HTML 1
TCGA_expression_clinical_combinator
evan199893 / TCGA_expression_clinical_combinator
Use this program can let user quickly combine the miRNA/Gene expression and clinical data. Speed up the data preprocessing step.
bioinformatics gene-expression mirna tcga tcga-data
Language:Python 1
kimdesok / DeepPATH
AI HUB Project: Classification of Lung Cancer Slide Images using Deep-Learning
wsi deep-learning tensorflow cancer-detection gene-mutations keras tcga-data tfrecords transfer-learning xception
Language:Jupyter Notebook 1
RRafiee / Bioconductor-GenomicDataCommons
Genomic Data Commons Query
tcga tcgabiolinks tcga-data lung lung-cancer methylation gene rna-seq adenoarcinoma gdc bioconductor
Language:R 1
shuzhenkuang / XGEP
XGEP for expression-based prediction of human essential genes and candidate lncRNAs in cancer cells
collaborative-filtering deep-learning essential-lncrnas human-essential-genes machine-learning tcga-data
Language:Python 1
YoannPa / biotab.manager
Scripts to manage biotab files from TCGA.
tcga tcga-data tcgabiolinks cancer-data bioinformatics
Language:R 1
Alberto-00 / Detection-signature-cancer
The Cancer Genome Atlas (TCGA), a cancer genomics reference program, has molecularly characterized more than 20,000 primary cancer samples and paired normal samples covering 33 types of cancer. This joint effort between the NCI and the National Human Genome Research Institute began in 2006.
cancer cancer-research cbioportal classification mutations siamese siamese-network signature-capture tcga tcga-data
Language:Python 0
niccolo99mandelli / SOPHYSM.jl
SOPHYSM - SOlid tumors PHYlogenetic Spatial Modeller - Julia GUI for Histological Analysis and Cancer Simulation
cancer-imaging-research cdsa histopathology-image-analysis image-processing simulator tcga-data jhistint jspace
Language:Julia 0
wanying4 / Computation-Analysis-of-TCGA-Cancer-Data
This project focuses on analyzing gene expression data from TCGA cancer data to derive associations among genes as well as disease phenotypes, co-expression signatures, and survival analysis.
cancer coexpression computational-genomics concordance-index gene-expression matlab mutual-information survival-analysis tcga-data
Language:MATLAB 0
ZarnackGroup / Elwakeel-et-al-2021
Supplementary R scripts for the manuscript "Disrupting PGE2/EP3 signaling in cancer-associated fibroblasts limits mammary carcinoma growth but promotes metastasis"
cancer-research survival-analysis survival-model tcga-data
Language:R 0

tcga-data

mahmoodlab / CLAM

BioinformaticsFMRP / TCGAbiolinks

MarvinLer / tcga_segmentation

PoisonAlien / TCGAmutations

sigven / oncoEnrichR

BioinformaticsFMRP / TCGAbiolinksGUI

rezacsedu / Multimodal-autoencoder-for-breast-cancer

KChen-lab / Texomer

waldronlab / MultiAssayWorkshop

HuaZou / bioinformatics_pipeline

MahShaaban / miRCancerdb

asmagen / SPAGEfinder

mschubert / TCGAbiolinks-downloader

deargen / DearWXpub

Eurus-Holmes / Tumor2Graph

bcgsc / tasrkleat-TCGA-analysis-scripts

jingxinfu / TCGAdnloader

mar-kan / thesis

ShixiangWang / ImmuneDR

urmi-21 / TCGA-Data-Analysis

ropensci / cRegulome

averissimo / tcga.data

aws-samples / aws-glue-athena-tcga

uazadi / TIDaC

WPZgithub / ConMod

adrian-aleks / TCGA-clasterization

Akenaide / wsoffcli

evan199893 / TCGA_expression_clinical_combinator

kimdesok / DeepPATH

RRafiee / Bioconductor-GenomicDataCommons

shuzhenkuang / XGEP

YoannPa / biotab.manager

Alberto-00 / Detection-signature-cancer

niccolo99mandelli / SOPHYSM.jl

wanying4 / Computation-Analysis-of-TCGA-Cancer-Data

ZarnackGroup / Elwakeel-et-al-2021