To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

IrisSpatialFeatures

DOI: 10.18129/B9.bioc.IrisSpatialFeatures    

This is the development version of IrisSpatialFeatures; to use it, please install the devel version of Bioconductor.

A package to extract spatial features based on multiplex IF images

Bioconductor version: Development (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>

Citation (from within R, enter citation("IrisSpatialFeatures")):

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 1.1.1
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_1.1.1.tar.gz
Windows Binary IrisSpatialFeatures_1.1.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) IrisSpatialFeatures_1.1.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/IrisSpatialFeatures
Package Short Url http://bioconductor.org/packages/IrisSpatialFeatures/
Package Downloads Report Download Stats

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