Stars
Repository for *Multimodal Network Diffusion Predicts Future Disease-Gene-Chemical Associations*
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 ris…
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 t…
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 wit…
A python tool to crawl snp information from UCSC and eqtl websites, including nearby snp functions, gene and other epigenomic informations, 2015
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
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 incl…
fastQTL analysis of methylation and expression data
This project is to build models to simultaneously analyze meQTLs and eQTLs
Hidden Markov Random Field Model - Inferring Gene-Disease Association by an Integrative Analysis of eQTL GWAS and Protein-Protein Interaction data
Free and Open source implementation of Bootstrap eQTL
Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging.
Differential expression analysis on TCGA samples.
A bioinformatics API to interface with public multi-omics bio databases for wicked fast data integration.
files from external sources used to populate Oncoscape database
IARC course on analyzing TCGA data in the SevenBridges Genomics CancerGenomicsCloud (SBG-CGC)
Scouring the Glioblastoma (GBM) TCGA expression data for molecular signatures indicative of survival benefit
Convert VCF (Variant Call Format) into TCGA MAF (Mutation Annotation Format)
R data package for pre-compiled somatic mutations from TCGA cohorts and CCLE
Download, integration and visualizations of the variety & volume of TCGA data.
Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
Python utilities for building integrated views of TCGA data.
TCGA data acquisition and processing for Project Cognoma
TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
Analysis of tissue-specific gene expression in GTEx dataset