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Bioconductor - mistyR (development version)

mistyR

This is the development version of mistyR; for the stable release version, see mistyR.

Multiview Intercellular SpaTial modeling framework

Bioconductor version: Development (3.22)

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] ORCID: 0000-0001-7177-1003 , Ricardo Omar Ramirez Flores [ctb] ORCID: 0000-0003-0087-371X , Philipp Schäfer [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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews BiomedicalInformatics, CellBiology, DecisionTree, Regression, SingleCell, Software, Spatial, SystemsBiology Version 1.17.0 In Bioconductor since BioC 3.13 (R-4.1) (4 years) License GPL-3 Depends R (>= 4.0) Imports assertthat, caret, deldir, digest, distances, dplyr (>= 1.1.0), filelock, furrr (>= 0.2.0), ggplot2, methods, purrr, ranger, readr (>= 2.0.0), ridge, rlang, rlist, R.utils, stats, stringr, tibble, tidyr, tidyselect (>= 1.2.0), utils, withr System Requirements URL https://saezlab.github.io/mistyR/ Bug Reports https://github.com/saezlab/mistyR/issues See More Suggests BiocStyle, covr, earth, future, igraph (>= 1.2.7), iml, kernlab, knitr, MASS, rmarkdown, RSNNS, testthat (>= 3.0.0), xgboost Linking To 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.

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