IrisSpatialFeatures

DOI: 10.18129/B9.bioc.IrisSpatialFeatures    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.8 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see IrisSpatialFeatures.

A package to extract spatial features based on multiplex IF images

Bioconductor version: 3.8

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 (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("IrisSpatialFeatures")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	FeatureExtraction, SingleCell, Software
Version	1.6.0
In Bioconductor since	BioC 3.6 (R-3.4) (1.5 years)
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
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Build Report

Package Archives

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

Source Package
Windows Binary
Mac OS X 10.11 (El Capitan)
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