mistyR

DOI: 10.18129/B9.bioc.mistyR    

Multiview Intercellular SpaTial modeling framework

Bioconductor version: Release (3.13)

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]

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

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

Installation

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

if (!requireNamespace("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, SystemsBiology
Version 1.0.2
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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://github.com/saezlab/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_1.0.2.tar.gz
Windows Binary mistyR_1.0.2.zip (64-bit only)
macOS 10.13 (High Sierra) mistyR_1.0.2.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
Old Source Packages for BioC 3.13 Source Archive

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