tohuangtao

tohuangtao's Stars

• PoisonAlien/maftools

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

  Language:R44722945219

• mdozmorov/TCGAsurvival

  Scripts to analyze TCGA data

  Language:R115101741

• PoisonAlien/TCGAmutations

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

  Language:R8751524

• IARCbioinfo/awesome-TCGA

  Curated list of TCGA resources

  51709

• RTCGA/RTCGA

  Download, integration and visualizations of the variety & volume of TCGA data.

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• waldronlab/curatedTCGAData

  Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

  Language:R446577

• BioinformaticsFMRP/TCGAWorkflow

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

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• cooperlab/TCGAIntegrator

  Python utilities for building integrated views of TCGA data.

  Language:Python325413

• JonnyTran/OpenOmics

  A bioinformatics API to interface with public multi-omics bio databases for wicked fast data integration.

  Language:Python3171613

• timflutre/eqtlbma

  Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging.

  Language:C++2292012

• cognoma/cancer-data

  TCGA data acquisition and processing for Project Cognoma

  Language:Jupyter Notebook20102428

• cbare/vcf2maf

  Convert VCF (Variant Call Format) into TCGA MAF (Mutation Annotation Format)

  Language:Python134216

• mforde84/RNAseq-Survival-Analysis-TCGA-KIRC

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• LichtargeLab/multimodal-network-diffusion

  Repository for *Multimodal Network Diffusion Predicts Future Disease-Gene-Chemical Associations*

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• theandygross/TCGA_differential_expression

  Differential expression analysis on TCGA samples.

  7304

• IARCbioinfo/SBG-CGC_course2018

  IARC course on analyzing TCGA data in the SevenBridges Genomics CancerGenomicsCloud (SBG-CGC)

  Language:R61574

• milospjanic/matrixeQTL2LocusZoom

  Script will use three parameters as inputs, 1) Gene ID from ENSEMBL annotation, 2) chromosome number where the gene is located 3) eQTL file from matrixeQTL and generate output for visualization with LocusZoom Plot containing rsIDs and p-values as columns 1 and 2.

  Language:Shell4201

• Sage-Bionetworks/Glioblastoma-Exploration

  Scouring the Glioblastoma (GBM) TCGA expression data for molecular signatures indicative of survival benefit

  Language:R41904

• milospjanic/PolygenicScoreCAD

  PolygenicScoreCAD is a bash/awk/R script for defining causality of a gene for coronary artery disease given the directionality of expression change in HCASMC with the increased global polygenic risk score. Script uses CAD GWAS data (Nelson et al.) and HCASMC eQTL data for regression analysis.

  Language:Shell320

• dnousome/eQTL-Brain

  eQTL (single and Meta analysis of Brain tissue)

  Language:R2102

• jknightlab/mePipe

  Functions to support running of Matrix-eQTL analysis pipeline. This includes support for adding principle components as covariates and determining the optimal number of principal components to include.

  Language:R2411

• SenZHANG-GitHub/snpSpider

  A python tool to crawl snp information from UCSC and eqtl websites, including nearby snp functions, gene and other epigenomic informations, 2015

  Language:Python2100

• swvanderlaan/fastQTLToolKit

  fastQTL analysis of methylation and expression data

  Language:Shell2502

• chrismckennan/Methylation_DNAVariation

  This project is to build models to simultaneously analyze meQTLs and eQTLs

  Language:Perl10

• CreRecombinase/BeQ2L

  Free and Open source implementation of Bootstrap eQTL

  Language:C++1301

• JunWangmath/GeP-HMRF

  Hidden Markov Random Field Model - Inferring Gene-Disease Association by an Integrative Analysis of eQTL GWAS and Protein-Protein Interaction data

  Language:R1000

• milospjanic/GeneCausalityTestCAD

  GeneCausalityTest for CAD (coronary artery disease) is a bash/awk/R script for defining causality of a gene for a given trait, in this case CAD, given the directionality of expression change with the increasing number of risk SNPs. Script uses CAD GWAS data (Nelson et al.) and HCASMC eQTL data for regression analysis.

  Language:Shell120

• nmchaves/tissue-specific-expression

  Analysis of tissue-specific gene expression in GTEx dataset

  Language:Jupyter Notebook1501

• oncoscape/TCGAarchive

  files from external sources used to populate Oncoscape database

  Language:JavaScript12

• vjcitn/bceQTL

  eQTL analysis of breast cancer, data and code underlying the PLoS One paper http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170181

  Language:R1