IrisSpatialFeatures

DOI: 10.18129/B9.bioc.IrisSpatialFeatures    

A package to extract spatial features based on multiplex IF images

Bioconductor version: Release (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>

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 1.3.0
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/
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