nipalsMCIA

DOI: 10.18129/B9.bioc.nipalsMCIA  

Multiple Co-Inertia Analysis via the NIPALS Method

Bioconductor version: Release (3.18)

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>

Installation

To install this package, start R (version "4.3") 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")

 

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

Details

biocViews	Classification, Clustering, MultipleComparison, Normalization, Preprocessing, SingleCell, Software
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
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
LinkingTo
Suggests	BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/Muunraker/nipalsMCIA
BugReports	https://github.com/Muunraker/nipalsMCIA/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	nipalsMCIA_1.0.0.tar.gz
Windows Binary	nipalsMCIA_1.0.0.zip
macOS Binary (x86_64)	nipalsMCIA_1.0.0.tgz
macOS Binary (arm64)	nipalsMCIA_1.0.0.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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive