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

Sparse Contrastive Principal Component Analysis

Bioconductor version: Development (3.20)

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] , Nima Hejazi [aut] , Sandrine Dudoit [ctb, ths]

Maintainer: Philippe Boileau <philippe_boileau at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Sparse contrastive principal component analysis HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, GeneExpression, Microarray, PrincipalComponent, RNASeq, Sequencing, Software
Version 1.19.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
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Suggests DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark
Linking To
Depends On Me OSCA.advanced, OSCA.workflows
Imports Me
Suggests Me
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Follow Installation instructions to use this package in your R session.

Source Package scPCA_1.19.0.tar.gz
Windows Binary
macOS Binary (x86_64) scPCA_1.19.0.tgz
macOS Binary (arm64) scPCA_1.19.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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