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nipalsMCIA
This is thereleased version of nipalsMCIA; for the devel version, seenipalsMCIA.
Multiple Co-Inertia Analysis via the NIPALS Method
Bioconductor version: Release (3.22)
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: 0000-0002-1233-1240, Joaquin Reyna [aut] ORCID: 0000-0002-8468-2840, Edel Aron [aut] ORCID: 0000-0002-8683-4772, Ferhat Ay [aut] ORCID: 0000-0002-0708-6914, Steven Kleinstein [aut] ORCID: 0000-0003-4957-1544, Anna Konstorum [aut] ORCID: 0000-0003-4024-2058
Maintainer: Maximilian Mattessich <maximilian.mattessich at northwestern.edu>
citation("nipalsMCIA")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("nipalsMCIA")For older versions of R, please refer to the appropriateBioconductor 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 | 1.8.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2 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 | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | nipalsMCIA_1.8.0.tar.gz |
| Windows Binary (x86_64) | nipalsMCIA_1.8.0.zip |
| macOS Binary (x86_64) | nipalsMCIA_1.8.0.tgz |
| macOS Binary (arm64) | nipalsMCIA_1.8.0.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 |