Introduction | Installation | Comparing PCA, SPCA, cPCA and scPCA | PCA | Sparse PCA | Contrastive PCA (cPCA) | Sparse Contrastive PCA (scPCA) | Cross-Validation for Hyperparameter Tuning of cPCA and scPCA | SPCA Optimization Frameworks | Bioconductor Integration via SingleCellExperiment | scPCA for Cell Cycle Effect Removal | Parallelization | Session Information | References
Package: scPCA 1.27.0
Philippe Boileau
scPCA: Sparse Contrastive Principal Component Analysis
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.
Authors:
scPCA_1.27.0.tar.gz
scPCA_1.27.0.zip(r-4.7)scPCA_1.27.0.zip(r-4.6)scPCA_1.27.0.zip(r-4.5)
scPCA_1.27.0.tgz(r-4.6-any)scPCA_1.27.0.tgz(r-4.5-any)
scPCA_1.27.0.tar.gz(r-4.7-any)scPCA_1.27.0.tar.gz(r-4.6-any)
scPCA_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scPCA/json (API)
| # Install 'scPCA' in R: |
| install.packages('scPCA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/philboileau/scpca/issues
Datasets:
- background_df - Simulated Background Data for cPCA and scPCA
- toy_df - Simulated Target Data for cPCA and scPCA
On BioConductor:scPCA-1.27.0(bioc 3.24)scPCA-1.26.0(bioc 3.23)
principalcomponentgeneexpressiondifferentialexpressionsequencingmicroarrayrnaseqbioconductorcontrastive-learningdimensionality-reduction
Last updated from:137ceaa607. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 214 | ||
| linux-devel-x86_64 | NOTE | 343 | ||
| source / vignettes | OK | 443 | ||
| linux-release-x86_64 | NOTE | 325 | ||
| macos-release-arm64 | NOTE | 207 | ||
| macos-oldrel-arm64 | NOTE | 166 | ||
| windows-devel | NOTE | 222 | ||
| windows-release | NOTE | 222 | ||
| windows-oldrel | NOTE | 211 | ||
| wasm-release | OK | 197 |
Exports:scPCA
Dependencies:abindassertthatBHBiocGenericsBiocParallelcliclustercodetoolscoopcpp11data.tableDelayedArraydigestdplyrelasticnetformatRfutile.loggerfutile.optionsfuturefuture.applygenericsglobalsglueIRangeskernlablambda.rlarslatticelifecyclelistenvmagrittrMatrixMatrixGenericsmatrixStatsorigamiparallellypillarpkgconfigpurrrR6rbibutilsRcppRcppEigenRdpackrlangRSpectrarsvdS4ArraysS4VectorsScaledMatrixsnowSparseArraysparsepcastringistringrtibbletidyselectutf8vctrswithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Simulated Background Data for cPCA and scPCA | background_df |
| Sparse Contrastive Principal Component Analysis | scPCA |
| Simulated Target Data for cPCA and scPCA | toy_df |
