vjcitn/ivygapseold

SummarizedExperiment for Ivy-GAP

ivygapSE

This package provides a SummarizedExperiment for Ivy-GAP metadata. See the ivyGlimpse app and an explanatory video.

The metadata and expression data are as distributed by Allen Institute for Brain Science as of 31 May 2017.

A brief vignette is available, and the ivyGlimpse() function will initiate a shiny app for exploring relationships between sub-block level image features quantified in 'subBlockDetails', survival time, and expression patterns. Essentially, one can use a scatterplot of a pair of image features to stratify the data.

ivyGlimpse will be accompanied by ivyTest, a tool for formally testing hypotheses relating image characteristics to expression patterns, and ivyBridge, which will emphasize interactive amalgamation of data and annotation related to glioblastoma.