IrisSpatialFeatures

DOI: 10.18129/B9.bioc.IrisSpatialFeatures    

A package to extract spatial features based on multiplex IF images

Bioconductor version: Release (3.6)

IrisSpatialFeatures reads the output of the PerkinElmer inForm software and calculates a variety of spatial statistics. In addition to simple counts, it can derive average nearest neighbors for each cell-type and interaction summary profiles for each celltype. These statistics are derived across images, both overall and regions of interest as defined by user defined masks.

Author: Daniel Gusenleitner, Jason L. Weirather

Maintainer: Daniel Gusenleitner <Daniel_Gusenleitner at dfci.harvard.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("IrisSpatialFeatures")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("IrisSpatialFeatures")

 

PDF	R Script	Vignette Title
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	FeatureExtraction, SingleCell, Software
Version	1.2.0
License	MIT + file LICENSE
Depends	R (>= 3.4)
Imports	Rcpp (>= 0.12.7), SpatialTools, gplots, spatstat, tiff, RColorBrewer, methods, grDevices, graphics, stats, utils, data.table, ggplot2, dplyr, magrittr, tibble
LinkingTo	Rcpp
Suggests	knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	IrisSpatialFeatures_1.2.0.tar.gz
Windows Binary	IrisSpatialFeatures_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	IrisSpatialFeatures_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/IrisSpatialFeatures
Package Short Url	http://bioconductor.org/packages/IrisSpatialFeatures/
Package Downloads Report	Download Stats