nipalsMCIA
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see nipalsMCIA.
Multiple Co-Inertia Analysis via the NIPALS Method
Bioconductor version: 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] , Ferhat Ay [aut] , Steven Kleinstein [aut] , Anna Konstorum [aut]
Maintainer: Maximilian Mattessich <maximilian.mattessich at northwestern.edu>
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 | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, MultipleComparison, Normalization, Preprocessing, SingleCell, Software |
| Version | 1.2.1 |
| 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 |
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.
| Source Package | nipalsMCIA_1.2.1.tar.gz |
| Windows Binary (x86_64) | nipalsMCIA_1.2.1.zip |
| macOS Binary (x86_64) | nipalsMCIA_1.2.1.tgz |
| macOS Binary (arm64) | nipalsMCIA_1.2.1.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 3.19 | Source Archive |