tcga-data | Topic | Ecosyste.ms: Repos

Topic: "tcga-data"

mahmoodlab/CLAM

Open source tools for computational pathology - Nature BME

Language: Python - Size: 45.8 MB - Last synced at: 5 days ago - Pushed at: about 1 month ago - Stars: 1,317 - Forks: 419

BioinformaticsFMRP/TCGAbiolinks

TCGAbiolinks

Language: R - Size: 349 MB - Last synced at: 5 days ago - Pushed at: about 1 month ago - Stars: 316 - Forks: 117

MarvinLer/tcga_segmentation

Whole Slide Image segmentation with weakly supervised multiple instance learning on TCGA | MICCAI2020 https://arxiv.org/abs/2004.05024

Language: Python - Size: 63.1 MB - Last synced at: 13 days ago - Pushed at: almost 4 years ago - Stars: 134 - Forks: 34

PoisonAlien/TCGAmutations

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

Language: R - Size: 449 MB - Last synced at: about 1 month ago - Pushed at: 8 months ago - Stars: 92 - Forks: 24

sigven/oncoEnrichR

Explore the cancer relevance of your gene list

Language: R - Size: 1.9 GB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 49 - Forks: 10

BioinformaticsFMRP/TCGAbiolinksGUI

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

Language: R - Size: 90.4 MB - Last synced at: 11 days ago - Pushed at: almost 4 years ago - Stars: 35 - Forks: 14

waldronlab/MultiAssayWorkshop

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

Language: TeX - Size: 2.78 MB - Last synced at: 11 months ago - Pushed at: over 1 year ago - Stars: 19 - Forks: 4

KChen-lab/Texomer

Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data

Language: R - Size: 32.9 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 19 - Forks: 8

rezacsedu/Multimodal-autoencoder-for-breast-cancer

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

Language: Python - Size: 23.3 MB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 19 - Forks: 9

mahmoodlab/CPATH_demographics

Demographic bias in misdiagnosis by computational pathology models - Nature Medicine

Language: Python - Size: 1.04 MB - Last synced at: 13 days ago - Pushed at: about 1 year ago - Stars: 13 - Forks: 2

HuaZou/bioinformatics_pipeline

Bioinformatics Pipeline

Language: R - Size: 5.73 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 9

MahShaaban/miRCancerdb

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

Language: R - Size: 1.37 MB - Last synced at: 21 days ago - Pushed at: over 7 years ago - Stars: 9 - Forks: 5

asmagen/SPAGEfinder

Computational approach to identify Survival associated Pairwise Gene Expression states.

Language: R - Size: 39.4 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 8 - Forks: 4

mschubert/TCGAbiolinks-downloader

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

Language: R - Size: 18.6 KB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 8 - Forks: 0

Eurus-Holmes/Tumor2Graph

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

Language: Python - Size: 3.83 MB - Last synced at: 6 days ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 0

deargen/DearWXpub

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

Language: R - Size: 15.7 MB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 6 - Forks: 4

jingxinfu/TCGAdnloader

TCGA hg19 and hg38 data downloader.

Language: Python - Size: 52.1 MB - Last synced at: 11 months ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 1

ShixiangWang/ImmuneDR 📦

A Community Curated Immune Resource Database in R format

Language: R - Size: 1.5 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 4 - Forks: 0

urmi-21/TCGA-Data-Analysis

Examples on processing and working with TCGA mutation and RNA-Seq data

Language: R - Size: 2.79 MB - Last synced at: about 1 year ago - Pushed at: about 6 years ago - Stars: 4 - Forks: 2

bcgsc/tasrkleat-TCGA-analysis-scripts

This repo stores codes for the analysis of tasrkleat results on TCGA RNA-Seq dataa

Language: Jupyter Notebook - Size: 181 MB - Last synced at: about 1 month ago - Pushed at: over 6 years ago - Stars: 4 - Forks: 1

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

Language: Python - Size: 22.9 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 3 - Forks: 0

mar-kan/thesis

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

Language: Jupyter Notebook - Size: 1.76 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 3 - Forks: 0

ropensci/cRegulome

An R package to access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer

Language: R - Size: 3.07 MB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 3 - Forks: 4

averissimo/tcga.data

Genomic data from TCGA ready to be used (organized per tissue type and in matrix form)

Language: R - Size: 18.9 MB - Last synced at: about 2 months ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 1

Akenaide/wsoffcli

POC ws-tcg scrapper

Language: HTML - Size: 158 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 1

YoannPa/biotab.manager

Scripts to manage biotab files from TCGA.

Language: R - Size: 117 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

WPZgithub/ConMod

Identifying conserved functional modules in multiple biological networks

Language: MATLAB - Size: 253 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

kimdesok/DeepPATH Fork of ncoudray/DeepPATH

AI HUB Project: Classification of Lung Cancer Slide Images using Deep-Learning

Language: Jupyter Notebook - Size: 25.9 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

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

Language: Jupyter Notebook - Size: 285 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 2

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.

Language: Python - Size: 33.2 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

shuzhenkuang/XGEP

XGEP for expression-based prediction of human essential genes and candidate lncRNAs in cancer cells

Language: Python - Size: 44.9 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

RRafiee/Bioconductor-GenomicDataCommons

Genomic Data Commons Query

Language: R - Size: 18 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

ArjunBasandrai/tcga-paad-survival-analysis

Survival Analysis on the TCGA-PAAD (The Cancer Genome Atlas-Pancreatic Adenocarcinoma) dataset

Language: Jupyter Notebook - Size: 20.3 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

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.

Language: Python - Size: 162 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1

niccolo99mandelli/SOPHYSM.jl

SOPHYSM - SOlid tumors PHYlogenetic Spatial Modeller - Julia GUI for Histological Analysis and Cancer Simulation

Language: Julia - Size: 5.93 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 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"

Language: R - Size: 618 KB - Last synced at: 15 days ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 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.

Language: MATLAB - Size: 472 KB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

fvalle1/topicTCGA

Notebooks for "A topic model analysis of TCGA transcriptomic data of breast and lung cancer"

Language: Jupyter Notebook - Size: 171 MB - Last synced at: about 1 month ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1

cristobalmitchell/hnsc-biomarkers

Statistical analysis of TCGA-HNSC miRNA sequences for identification of biomarkers indicating lymphovascular invasion presence across clinical stages

Language: R - Size: 6.76 MB - Last synced at: 6 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

fvalle1/master_thesis 📦

Language: Jupyter Notebook - Size: 131 MB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 1