PoisonAlien/maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

Language: R - Size: 70.1 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 421 - Forks: 215

liupei101/Pipeline-Processing-TCGA-Slides-for-MIL

This repo provides an exhaustive pipeline of processing TCGA whole-slide images for downstream multiple instance learning.

Language: Python - Size: 14.8 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 18 - Forks: 6

YoannPa/biotab.manager

Scripts to manage biotab files from TCGA.

Language: R - Size: 117 KB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 1 - Forks: 0

Bioconductor/GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.

Language: R - Size: 4.38 MB - Last synced: 7 days ago - Pushed: 9 days ago - Stars: 82 - Forks: 23

pipaber/Multi-omics

This is a repository to show my experience analyzing different kinds of Omics data.

Language: JavaScript - Size: 5.46 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0

waldronlab/MultiAssayExperiment

Bioconductor package for management of multi-assay data

Language: R - Size: 6.86 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 68 - Forks: 32

waldronlab/TCGAutils

Toolbox package for organizing and working with TCGA data

Language: R - Size: 753 KB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 21 - Forks: 6

BioinformaticsFMRP/TCGAbiolinks

TCGAbiolinks

Language: R - Size: 349 MB - Last synced: 5 days ago - Pushed: about 1 month ago - Stars: 275 - Forks: 107

ayueme/easyTCGA

Make TCGA download and prepare easy!

Language: R - Size: 5.38 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 70 - Forks: 9

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: 17 days ago - Pushed: about 2 months ago - Stars: 0 - Forks: 1

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: 2 days ago - Pushed: almost 3 years ago - Stars: 113 - Forks: 34

sales-lab/omicsdata

Support package for the "Omics Data" course

Language: R - Size: 42 KB - Last synced: 2 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 1

nuno-agostinho/psichomics

Interactive R package to quantify, analyse and visualise alternative splicing

Language: R - Size: 56.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 33 - Forks: 12

mariachiaragrieco/bulk-RNAseq

bulk-RNAseq analysis for Transcriptomics Course 2021 (MSc Bioinformatics for Computational Genomics)

Language: HTML - Size: 5.96 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

ropensci/UCSCXenaTools

:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/

Language: R - Size: 2.86 MB - Last synced: 4 days ago - Pushed: 4 months ago - Stars: 98 - Forks: 12

greenelab/BioBombe

BioBombe: Sequentially compressed gene expression features enhances biological signatures

Language: Jupyter Notebook - Size: 2.28 GB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 61 - Forks: 23

Neal-Liu1/Multi-omics-integration

Contains code related to my multi-omics integration project at WEHI.

Language: R - Size: 136 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

swiri021/Xena_wrapper

xenaPython wrapper

Language: Python - Size: 1.57 MB - Last synced: about 2 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

RobinPetit/Breast-Cancer-Purity

Study of breast cancer purity

Language: TeX - Size: 1.45 MB - Last synced: 2 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

msls-bioinfo/CmiRClustFinder_v1.0

CmiRClustFinder v1.0: a tool for identification of CNV co-locolized miRNA, miRNA clusers and genes in TCGA cancer cohorts.

Language: R - Size: 127 KB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 3 - Forks: 14

Caleydo/tdp_publicdb

Database connector for the bioinfoDB.hg38 database

Language: TypeScript - Size: 4.92 MB - Last synced: 13 days ago - Pushed: 3 months ago - Stars: 1 - Forks: 3

iVis-at-Bilkent/pathway-mapper

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

Language: TypeScript - Size: 65.8 MB - Last synced: 21 days ago - Pushed: about 2 months ago - Stars: 55 - Forks: 28

web4bio/webgen

WebGen Vertically Integrated Project

Language: JavaScript - Size: 20.5 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 11 - Forks: 26

Moha-cm/RNAseq-Analysis

Bulk Rna-seq Analysis

Language: HTML - Size: 4.4 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

dmis-lab/VAECox

ISMB 2020: Improved survival analysis by learning shared genomic information from pan-cancer data

Language: Python - Size: 85.5 MB - Last synced: 2 days ago - Pushed: almost 4 years ago - Stars: 15 - Forks: 9

genepattern/TCGA.SampleSelection

TCGA.SampleSelection wrapper module for GenePattern.

Language: R - Size: 10.5 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 1

cognoma/cancer-data

TCGA data acquisition and processing for Project Cognoma

Language: Jupyter Notebook - Size: 19.4 MB - Last synced: 14 days ago - Pushed: about 6 years ago - Stars: 21 - Forks: 28

rashindrie/ANSAC

Classification of whole-slide images based on tumor infiltrating lymphocyte grades using image-level labels

Language: Python - Size: 354 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

histolab/gdc-api-wrapper

Genomic Data Commons API wrapper

Language: Python - Size: 32.2 KB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 5 - Forks: 0

seahurt/tcga-utils

Some tools to handle tcga data

Language: Python - Size: 2.94 MB - Last synced: 6 months ago - Pushed: about 5 years ago - Stars: 1 - Forks: 0

kevinhu/cancer_data

A unified downloader+preprocessor for cancer genomics datasets

Language: Python - Size: 669 KB - Last synced: 8 days ago - Pushed: about 1 month ago - Stars: 14 - Forks: 6

bpark-research/TCGA_Spark

Language: Jupyter Notebook - Size: 1.61 MB - Last synced: 6 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

ZJUFanLab/CCL-cGPS

A clinical genomics-guided prioritizing strategy enables accurately selecting proper cancer cell lines for biomedical research

Language: R - Size: 593 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 8 - Forks: 1

matteocereda/GSECA

Gene Set Enrichment Class Analysis for heterogeneous RNA sequencing data

Language: R - Size: 56.4 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 5 - Forks: 0

KarakulakTulay/gtex-tcga-data-download

Describes how to download RNA-Seq controlled data from GTEx via sra-toolkit and from TCGA via GDC Data Transfer Tool

Size: 14.6 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 0

hclimente/smartas

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

Language: Jupyter Notebook - Size: 504 MB - Last synced: 7 months ago - Pushed: about 6 years ago - Stars: 14 - Forks: 5

deargen/DearCascadedWx

Public codes for Cascaded Wx algorithm to select genes relative with patients survivals.

Language: Python - Size: 24.5 MB - Last synced: 7 months ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 2

cdiener/proliferation

Project to study proliferation and metabolic liabilities across several thousand cancer samples.

Language: R - Size: 29.2 MB - Last synced: 7 months ago - Pushed: about 7 years ago - Stars: 0 - Forks: 3

BioinformaticsFMRP/TCGAWorkflowData

Example data to TCGAWorkflow

Language: R - Size: 125 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 4 - Forks: 5

MartheLaisne/TCGA_Adam12_IkrameProject

Projet Ikrame : Nanostring, Activation du gène TSPS ADAM12 par TAK1 et KAT2A

Size: 19.3 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

cpreid2/gdc-rnaseq-tool 📦

Tool to download/merge RNASeq data from the GDC Portal in matrices identified by TCGA barcode

Language: Python - Size: 3.39 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 33 - Forks: 14

tjiagoM/gtex-transcriptome-modelling

Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits

Language: Jupyter Notebook - Size: 53 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 9 - Forks: 2

cumbof/TCGA2BED

The Cancer Genome Atlas Data Extraction and Conversion Tool

Language: Java - Size: 14.9 MB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 2

RRafiee/Bioconductor-GenomicDataCommons

Genomic Data Commons Query

Language: R - Size: 18 MB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 0

greenelab/pancancer

Building classifiers using cancer transcriptomes across 33 different cancer-types

Language: Jupyter Notebook - Size: 28.8 MB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 115 - Forks: 59

knightlab-analyses/mycobiome

Pan-cancer mycobiome atlas

Language: Jupyter Notebook - Size: 2.07 GB - Last synced: 5 months ago - Pushed: over 1 year ago - Stars: 16 - Forks: 12

BioinformaticsFMRP/Bioc2017.TCGAbiolinks.ELMER

Integrative analysis workshop with TCGAbiolinks and ELMER

Size: 113 MB - Last synced: 8 months ago - Pushed: almost 7 years ago - Stars: 6 - Forks: 0

texchi2/pvalueTex

Supplementary Material of manuscript, and Cutoff Finding R script

Language: R - Size: 22 MB - Last synced: 4 months ago - Pushed: over 2 years ago - Stars: 4 - Forks: 1

cumbof/OpenGDC

An open-source Java tool to automatically extract and convert all clinical and genomic data from the Genomic Data Commons to BED, GTF, CSV, and JSON format

Language: Java - Size: 237 MB - Last synced: 8 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 1

bernardo-de-almeida/PanCancer_CentrosomeAmplification

Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome

Size: 22.5 MB - Last synced: 10 months ago - Pushed: almost 3 years ago - Stars: 4 - Forks: 4

BioinformaticsFMRP/TCGAWorkflow

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

Language: TeX - Size: 36.9 MB - Last synced: 7 months ago - Pushed: 11 months ago - Stars: 38 - Forks: 20

aozh7/SmulTCan

Survival TXT files for the 33 TCGA datasets

Size: 612 KB - Last synced: 17 days ago - Pushed: over 2 years ago - Stars: 2 - Forks: 2

vjcitn/BiocOV

An overview of Bioconductor with applications to multiomics, genome representation, and single-cell biologiy

Language: R - Size: 4.31 MB - Last synced: 5 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 1

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: about 1 year ago - Pushed: over 5 years ago - Stars: 4 - Forks: 0

mariachiaragrieco/TCGAclassification

Python project for classification of normal vs tumoral samples using TCGA gene expression data for Scientific Programming Course 2021 (MSc Bioinformatics for Computational Genomics)

Language: Jupyter Notebook - Size: 697 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

pasmopy/breast_cancer

Imoto et al., A text-based computational framework for patient -specific modeling for classification of cancers. iScience 25, 103944 (2022). https://doi.org/10.1016/j.isci.2022.103944

Language: Python - Size: 302 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 3 - Forks: 5

cognoma/cognoma

Putting machine learning in the hands of cancer biologists

Language: Jupyter Notebook - Size: 5.3 MB - Last synced: 14 days ago - Pushed: over 6 years ago - Stars: 96 - Forks: 31

t-silvers/casskit

casskit: cancer association studies toolkit

Language: Python - Size: 517 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

Arshammik/Bioinformatics

Courses, projects and challenges in bioinformatics,

Language: Python - Size: 14.7 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 3 - Forks: 0

inab/mg-process_TCGA_CD 📦

TCGA Cancer Detection (for MuG/VRE OpenEBench installation)

Language: Python - Size: 1020 KB - Last synced: 22 days ago - Pushed: almost 5 years ago - Stars: 0 - 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: about 1 year ago - Pushed: about 2 years ago - Stars: 3 - Forks: 0

waldronlab/MultiAssayExperiment.TCGA

Language: R - Size: 572 KB - Last synced: 15 days ago - Pushed: almost 1 year ago - Stars: 7 - Forks: 4

bblodfon/paad-survival-bench

Benchmark survival ML models against a multimodal TCGA dataset

Language: R - Size: 155 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

selcenari/ceRNAnetsim

Simulation of interactions miRNA:Competing Targets

Language: R - Size: 28.9 MB - Last synced: 7 days ago - Pushed: 3 months ago - Stars: 4 - Forks: 2

rezacsedu/Neural-Ensemble-Method-for-Cancer-Prediction

A Snapshot Neural Ensemble Method for Cancer Type Prediction Based on Copy Number Variations

Language: Jupyter Notebook - Size: 20.8 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 19 - Forks: 9

meji9086/TCGA-Data-Analysis

cancer mRNAseq data analysis

Language: Jupyter Notebook - Size: 8.72 MB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 2

CasillasAlba/GeneFlow

GeneFlow is a scalable and flexible software library that encompasses data acquisition methods, preprocessing techniques, data analytics, data visualization, and Machine Learning algorithms that can be applied to genomic data.

Language: Jupyter Notebook - Size: 8.94 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

AndrewGarven/DifferentialExpression

RNA-sequencing differential expression analysis (Deseq2 & edgeR)

Language: R - Size: 3.57 MB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

inab/TCGA_benchmarking_workflow

Language: HTML - Size: 7.31 MB - Last synced: 22 days ago - Pushed: about 1 year ago - Stars: 3 - Forks: 4

HuaZou/TCGA_HNSC

An immune-related gene prognostic index for head and neck squamous cell carcinoma

Language: HTML - Size: 18.5 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

u-brite/o-miner

Patient stratification and molecular mechanism identification using patient clinotypes and transcriptomics embeddings

Language: Jupyter Notebook - Size: 26.4 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 1

cumbof/OpenGDC.py

Python implementation of the OpenGDC software https://github.com/cumbof/OpenGDC

Language: Python - Size: 94.9 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

choilab-jefferson/TCGA_pipeline

Radiomics pipeline for TCGA datasets

Language: Nextflow - Size: 15.6 KB - Last synced: 8 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

SalamOsman/Creating-a-meta-file-from-TCGA-raw-clinical-file

Workflow for handling TCGA clinical data in R

Language: R - Size: 29.3 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

SanandhKumar02/MiniProject_ProstateCancer

Prostate Cancer Biomarker Identification using Machine learning approach

Language: Jupyter Notebook - Size: 41.2 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

amarinderthind/mutation_load_comparison_plot

This plot is useful for the comparison of mutational load across the cancer types, with input data in 2 coulmns i.e cancer types and mutatonal load for each samples in specificed cancer type.

Language: R - Size: 13.7 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

4DtyU/R-scripting-samples_AnnaBird

Example code supporting immunology research

Language: HTML - Size: 11 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

dogmaticcentral/CG

CG - cancer genomics pipeline

Language: Python - Size: 37.6 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 5 - Forks: 4

inab/TCGA_benchmarking_dockers

OpenEBench TCGA benchmarking Docker declarations

Language: Python - Size: 4.34 MB - Last synced: 22 days ago - Pushed: over 2 years ago - Stars: 1 - Forks: 4

texchi2/hnscc

HNSCC survival analysis

Language: R - Size: 873 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 2 - Forks: 0

Anustup900/Histopathology-cancer-image-data-exploration-and-detection-by-deep-learning-VGG-16-CNN

Data Exploration , visualization and deep learning detection as well classification of Histopathology image of cancers by CNN-VGG16 on tcga data set

Language: Jupyter Notebook - Size: 2.28 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 2 - Forks: 0

ionut-d/ML_TCGA_data_mining_Wnt_signalling_ColoRectalCancer

UNSUPERVISED MACHINE LEARNING (CLUSTERING): TCGA data mining for studying the system of interactions between sub-branches of Wnt signalling pathway in colorectal cancer

Language: R - Size: 16.6 KB - Last synced: 12 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 1

salzmanlab-admin/DEEPEST-Fusion

DEEPEST-Fusion is a fusion detection algorithm specially designed for screening massive cancer sequencing databases

Language: R - Size: 10 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 4 - Forks: 5

cgplab/PAMESdata

Precomputed informative CpG sites and CpG islands to be used with PAMES package

Language: R - Size: 39.9 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 2

MI2DataLab/KRAB_ZNF

KRAB-ZNF explorer - expression of KRAB-ZNF- transcription factors in The Cancer Genome Atlas study

Language: HTML - Size: 454 MB - Last synced: 22 days ago - Pushed: almost 5 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: about 1 year ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

vsundesha/TCGA_benchmarking_workflow Fork of inab/TCGA_benchmarking_workflow

Size: 5.47 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

gwaybio/pancan_viz

Visualizing TCGA pancancer datasets

Language: Jupyter Notebook - Size: 16.7 MB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 1 - Forks: 1

lcolladotor/recount-brain-bog19

Poster for Biology of Genomes 2019 (#bog19) on recount-brain

Language: HTML - Size: 3.33 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 3

HFooladi/tybalt Fork of greenelab/tybalt

Training and evaluating a variational autoencoder for pan-cancer gene expression data

Language: Jupyter Notebook - Size: 67.2 MB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 1

tjbencomo/TBmisc

Another R package with tools for working with biomedical data

Language: R - Size: 451 KB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

gibsramen/TCGA-metadata

Collection of up-to-date metadata from TCGA.

Size: 7.41 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

aryeelab/tcgaWGBSData.hg19

Language: R - Size: 17.6 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

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: 4 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 1

minesh1291/BigData-Appspot

Size: 1.95 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

minesh1291/isb-cgc-dash-prep

Size: 8.79 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

metamaden/gdc_download_tools

Directions and code for generic GDC data downloads.

Size: 3.23 MB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0