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nipalsMCIA

Multiple Co-Inertia Analysis via the NIPALS Method


Bioconductor version: Release (3.19)

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] , Joaquin Reyna [aut] , Edel Aron [aut] , Anna Konstorum [aut]

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

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

Installation

To install this package, start R (version "4.4") and enter:


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

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")
Analysis of MCIA Decomposition HTML R Script
Predicting New MCIA scores HTML R Script
Single Cell Analysis HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Clustering, MultipleComparison, Normalization, Preprocessing, SingleCell, Software
Version 1.2.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 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
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Suggests BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package nipalsMCIA_1.2.0.tar.gz
Windows Binary nipalsMCIA_1.2.0.zip (64-bit only)
macOS Binary (x86_64) nipalsMCIA_1.2.0.tgz
macOS Binary (arm64) nipalsMCIA_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/nipalsMCIA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/nipalsMCIA
Bioc Package Browser https://code.bioconductor.org/browse/nipalsMCIA/
Package Short Url https://bioconductor.org/packages/nipalsMCIA/
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