mistyR

DOI: 10.18129/B9.bioc.mistyR    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see mistyR.

Multiview Intercellular SpaTial modeling framework

Bioconductor version: 3.14

mistyR is an implementation of the Multiview Intercellular SpaTialmodeling framework (MISTy). MISTy is an explainable machine learning framework for knowledge extraction and analysis of single-cell, highly multiplexed, spatially resolved data. MISTy facilitates an in-depth understanding of marker interactions by profiling the intra- and intercellular relationships. MISTy is a flexible framework able to process a custom number of views. Each of these views can describe a different spatial context, i.e., define a relationship among the observed expressions of the markers, such as intracellular regulation or paracrine regulation, but also, the views can also capture cell-type specific relationships, capture relations between functional footprints or focus on relations between different anatomical regions. Each MISTy view is considered as a potential source of variability in the measured marker expressions. Each MISTy view is then analyzed for its contribution to the total expression of each marker and is explained in terms of the interactions with other measurements that led to the observed contribution.

Author: Jovan Tanevski [cre, aut] , Ricardo Omar Ramirez Flores [ctb] , Philipp Schäfer [ctb]

Maintainer: Jovan Tanevski <jovan.tanevski at uni-heidelberg.de>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("mistyR")

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("mistyR")

 

HTML	R Script	Getting started
PDF	R Script	mistyR and SpatialExperiment
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiomedicalInformatics, CellBiology, DecisionTree, Regression, SingleCell, Software, Spatial, SystemsBiology
Version	1.2.1
In Bioconductor since	BioC 3.13 (R-4.1) (1 year)
License	GPL-3
Depends	R (>= 4.0)
Imports	assertthat, caret, deldir, digest, distances, dplyr, filelock, furrr (>= 0.2.0), ggplot2, MASS, purrr, ranger, readr, rlang, rlist, R.utils, stats, stringr, tibble, tidyr, withr
LinkingTo
Suggests	BiocStyle, covr, future, igraph, knitr, Matrix, progeny, rmarkdown, sctransform, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://saezlab.github.io/mistyR/
BugReports	https://github.com/saezlab/mistyR/issues
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	mistyR_1.2.1.tar.gz
Windows Binary	mistyR_1.2.1.zip
macOS 10.13 (High Sierra)	mistyR_1.2.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mistyR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mistyR
Package Short Url	https://bioconductor.org/packages/mistyR/
Package Downloads Report	Download Stats