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 (3.21)

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: ), Joaquin Reyna [aut] (ORCID: ), Edel Aron [aut] (ORCID: ), Ferhat Ay [aut] (ORCID: ), Steven Kleinstein [aut] (ORCID: ), Anna Konstorum [aut] (ORCID: )

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Clustering, MultipleComparison, Normalization, Preprocessing, SingleCell, Software
Version	1.5.0
In Bioconductor since	BioC 3.18 (R-4.3) (1 year)
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

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.

Source Package	nipalsMCIA_1.5.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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/
Package Downloads Report	Download Stats