IrisSpatialFeatures

DOI: 10.18129/B9.bioc.IrisSpatialFeatures    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see IrisSpatialFeatures.

A package to extract spatial features based on multiplex IF images

Bioconductor version: 3.7

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	1.3.0
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
Links To Me
Build Report

Package Archives

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

Source Package	IrisSpatialFeatures_1.3.0.tar.gz
Windows Binary	IrisSpatialFeatures_1.3.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	IrisSpatialFeatures_1.3.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/IrisSpatialFeatures
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IrisSpatialFeatures
Package Short Url	http://bioconductor.org/packages/IrisSpatialFeatures/
Package Downloads Report	Download Stats