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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, MultipleComparison, Normalization, Preprocessing, SingleCell, Software |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 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 | tidyexposomics |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | nipalsMCIA_1.11.0.tar.gz |
| Windows Binary (x86_64) | nipalsMCIA_1.11.0.zip |
| macOS Binary (big-sur-x86_64) | nipalsMCIA_1.11.0.tgz |
| macOS Binary (sonoma-arm64) | nipalsMCIA_1.11.0.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 |