genomeVerse

Umbrella package for Genomic data Processing and Analysis

Axel S. Martin, Karissa Whiting, Arshi Arora, Margaret Hannum
Oct 1, 2020 R Package

genomeVerse: Framework for Genomic data Processing and Analysis

genomeVerse is an umbrella package for genomic data processing and analysis with the genomeVerse ecosystem of R packages developed in the department of Epidemiology & Biostatistics at Memorial Sloan Kettering Cancer Center.

The library(genomeVerse) loads the following packages:

  • gnomeR for data downloading and processing from cBioPortal a genomic tool distributed by Memorial Sloan Kettering Cancer Center. The source code can be found on github.
  • panelmap creates panels for summarizing binary data, categorical data (more than 2 categories) and continuous data for known groups. panelmap is a visual aid to understand associations and trends in data instead from tedious tables and trying to infer multiple plots. The source code can be found on github.
  • survClust an outcome weighted supervised clustering algorithm, designed to classify patients according to their molecular as well as time-event or end point of interest. We present classification of samples on molecular data supervised by time-event data like Overall Survival (OS), Progression Free Survival etc.
  • OncoCast an ensemble learner for survival prediction and stratification with improved interface. Allows for multiple machine learning to be applied to a high-dimensional data set with survival outcome (including left-truncated data).
  • iClusterPlus Programs iClusterPlus and iClusterBayes are developed for integrative clustering analysis of multi-type genomic data, which are significant extension of the iCluster program (Shen, Olshen and Ladanyi, 2009). Multi-type genomic data arise from the experiments where biological samples (e.g., tumor samples) are analyzed by multiple techniques, for instance, array comparative genomic hybridization (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so on. Examples of these data can be obtained from the Cancer Genome Atlas (TCGA) (http://cancergenome.nih.gov/).

Installation

# install.packages("devtools")
devtools::install_github("AxelitoMartin/genomeVerse")
R package Genomics Analytics
Axel S. Martin
Axel S. Martin
PhD Student

My research interests include developing doubly-robust estimator theory for transportability and generalization of treatment specific survival curves, and developing doubly-robust estimators in the context of repeated continuous/factorial exposures effects.