IrisSpatialFeatures
This package is for version 3.6 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: 3.6
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("IrisSpatialFeatures")):
Installation
To install this package, start R (version "3.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("IrisSpatialFeatures")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("IrisSpatialFeatures")| Vignette Title | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | FeatureExtraction, SingleCell, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/IrisSpatialFeatures |
| Package Short Url | https://bioconductor.org/packages/IrisSpatialFeatures/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |