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Bioconductor - scPCA (development version)

scPCA

This is the development version of scPCA; for the stable release version, see scPCA.

Sparse Contrastive Principal Component Analysis

Bioconductor version: Development (3.22)

A toolbox for sparse contrastive principal component analysis (scPCA) of high-dimensional biological data. scPCA combines the stability and interpretability of sparse PCA with contrastive PCA's ability to disentangle biological signal from unwanted variation through the use of control data. Also implements and extends cPCA.

Author: Philippe Boileau [aut, cre, cph] ORCID: 0000-0002-4850-2507 , Nima Hejazi [aut] ORCID: 0000-0002-7127-2789 , Sandrine Dudoit [ctb, ths] ORCID: 0000-0002-6069-8629

Maintainer: Philippe Boileau <philippe_boileau at berkeley.edu>

Citation (from within R, enter citation("scPCA")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("scPCA")

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("scPCA")
Details biocViews DifferentialExpression, GeneExpression, Microarray, PrincipalComponent, RNASeq, Sequencing, Software Version 1.23.0 In Bioconductor since BioC 3.10 (R-3.6) (5.5 years) License MIT + file LICENSE Depends R (>= 4.0.0) Imports stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami, RSpectra, coop, Matrix, DelayedArray, ScaledMatrix, MatrixGenerics System Requirements URL https://github.com/PhilBoileau/scPCA Bug Reports https://github.com/PhilBoileau/scPCA/issues See More Suggests DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark Linking To Enhances Depends On Me OSCA.advanced, OSCA.workflows Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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