mgcca
This is the development version of mgcca; to use it, please install the devel version of Bioconductor.
Generalized Canonical Correlation Analysis with Missing Individuals
Bioconductor version: Development (3.24)
Implements Generalized Canonical Correlation Analysis (GCCA) with missing individuals (whole missing rows; van de Velden and Bijmolt, 2006) for multi-block omics integration. The package operates directly on HDF5 matrices via the BigDataStatMeth C++ API to scale computations; R functions are thin wrappers around the C++ core.
Author: Dolors Pelegri-Siso [aut, cre] 
, Isaac Subirana [aut], Juan R. Gonzalez [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri at isglobal.org>
citation("mgcca")):Dolors Pelegri-Siso, Isaac Subirana, Juan R. Gonzalez. mgcca: Generalized Canonical Correlation Analysis with Missing Individuals. doi:10.18129/B9.bioc.mgcca, R package version 0.99.7, https://bioconductor.org/packages/mgcca.
Generated from the package metadata; it may differ from the package's own citation.
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("mgcca")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("mgcca")| Generalized Canonical Correlation with missing individuals - Examples | HTML |
| How much of a shared subspace is carried by group structure? | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | DimensionReduction, Epigenetics, GeneExpression, Metabolomics, PrincipalComponent, Software, StatisticalMethod, Transcriptomics |
| Version | 0.99.7 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | BigDataStatMeth (>= 2.0.6), MASS, rlang (>= 1.1.0), withr, Rcpp (>= 1.0.6), ggplot2 (>= 3.4.0), ggthemes, impute, SummarizedExperiment, graphics, grDevices, grid, methods, stats, utils |
| System Requirements | GNU make, C++17 |
| URL | https://isglobal-brge.github.io/mgcca/ https://github.com/isglobal-brge/mgcca http://brge.isglobal.org |
| Bug Reports | https://github.com/isglobal-brge/mgcca/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), MultiAssayExperiment, Biobase, wordcloud, GenomicRanges, IRanges, BiocGenerics, made4, RSpectra, GenomeInfoDb, curatedTCGAData, TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db |
| Linking To | Rcpp, RcppEigen, Rhdf5lib, BigDataStatMeth, BH |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/mgcca |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/mgcca |
| Package Short Url | https://bioconductor.org/packages/mgcca/ |
| Package Downloads Report | Download Stats |