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Bioconductor - nipalsMCIA (development version)

nipalsMCIA

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

Multiple Co-Inertia Analysis via the NIPALS Method

Bioconductor version: Development (3.22)

Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the Nonlinear Iterative Partial Least Squares method (NIPALS) proposed in (Hanafi et. al, 2010). Allows multiple options for row- and table-level preprocessing, and speeds up computation of variance explained. Vignettes detail application to bulk- and single cell- multi-omics studies.

Author: Maximilian Mattessich [cre] ORCID: 0000-0002-1233-1240 , Joaquin Reyna [aut] ORCID: 0000-0002-8468-2840 , Edel Aron [aut] ORCID: 0000-0002-8683-4772 , Ferhat Ay [aut] ORCID: 0000-0002-0708-6914 , Steven Kleinstein [aut] ORCID: 0000-0003-4957-1544 , Anna Konstorum [aut] ORCID: 0000-0003-4024-2058

Maintainer: Maximilian Mattessich <maximilian.mattessich at northwestern.edu>

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

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("nipalsMCIA")
Details biocViews Classification, Clustering, MultipleComparison, Normalization, Preprocessing, SingleCell, Software Version 1.7.0 In Bioconductor since BioC 3.18 (R-4.3) (1.5 years) License GPL-3 Depends R (>= 4.3.0) Imports ComplexHeatmap, dplyr, fgsea, ggplot2 (>= 3.0.0), graphics, grid, methods, MultiAssayExperiment, SummarizedExperiment, pracma, rlang, RSpectra, scales, stats System Requirements URL https://github.com/Muunraker/nipalsMCIA Bug Reports https://github.com/Muunraker/nipalsMCIA/issues See More Suggests BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) 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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