SpatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data.

ABSTRACT:

Summary

Multiplex immunofluorescence (mIF) staining combined with quantitative digital image analysis is a novel and increasingly used technique that allows for the characterization of the tumor immune microenvironment (TIME). Generally, mIF data is used to examine the abundance of immune cells in the TIME; however, this does not capture spatial patterns of immune cells throughout the TIME, a metric increasingly recognized as important for prognosis. To address this gap, we developed an R package spatialTIME that enables spatial analysis of mIF data, as well as the iTIME web application that provides a robust but simplified user interface for describing both abundance and spatial architecture of the TIME. The spatialTIME package calculates univariate and bivariate spatial statistic

SUBMITTER: Creed JH 

PROVIDER: S-EPMC8652029 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature