scITD: Single-Cell Interpretable Tensor Decomposition

Single-cell Interpretable Tensor Decomposition (scITD) employs the Tucker tensor decomposition to extract multicell-type gene expression patterns that vary across donors/individuals. This tool is geared for use with single-cell RNA-sequencing datasets consisting of many source donors. The method has a wide range of potential applications, including the study of inter-individual variation at the population-level, patient sub-grouping/stratification, and the analysis of sample-level batch effects. Each "multicellular process" that is extracted consists of (A) a multi cell type gene loadings matrix and (B) a corresponding donor scores vector indicating the level at which the corresponding loadings matrix is expressed in each donor. Additional methods are implemented to aid in selecting an appropriate number of factors and to evaluate stability of the decomposition. Additional tools are provided for downstream analysis, including integration of gene set enrichment analysis and ligand-receptor analysis. Tucker, L.R. (1966) <doi:10.1007/BF02289464>. Unkel, S., Hannachi, A., Trendafilov, N. T., & Jolliffe, I. T. (2011) <doi:10.1007/s13253-011-0055-9>. Zhou, G., & Cichocki, A. (2012) <doi:10.2478/v10175-012-0051-4>.

Version: 1.0.2
Depends: R (≥ 4.0.0), Matrix
Imports: rTensor, ica, fgsea, circlize, reshape2, parallel, ComplexHeatmap, ggplot2, mgcv, utils, Rcpp, RColorBrewer, dplyr, edgeR, sva, stats, Rmisc, ggpubr, msigdbr, sccore, NMF
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
Suggests: methods, knitr, rmarkdown, testthat, coda.base, grid, ssvd, simplifyEnrichment, WGCNA, cowplot, matrixStats, stringr, zoo, rlang, AnnotationDbi, GO.db, conos, pagoda2, betareg, slam, tm
Published: 2022-03-23
Author: Jonathan Mitchel [cre, aut], Evan Biederstedt [aut], Peter Kharchenko [aut]
Maintainer: Jonathan Mitchel <jonathan.mitchel3 at gmail.com>
License: GPL-3
NeedsCompilation: yes
Materials: README
CRAN checks: scITD results

Documentation:

Reference manual: scITD.pdf

Downloads:

Package source: scITD_1.0.2.tar.gz
Windows binaries: r-devel: scITD_1.0.2.zip, r-release: scITD_1.0.2.zip, r-oldrel: scITD_1.0.2.zip
macOS binaries: r-release (arm64): scITD_1.0.2.tgz, r-release (x86_64): scITD_1.0.2.tgz, r-oldrel: not available
Old sources: scITD archive

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