TCA: Tensor Composition Analysis

Tensor Composition Analysis (TCA) allows the deconvolution of two-dimensional data (features by observations) coming from a mixture of heterogeneous sources into a three-dimensional matrix of signals (features by observations by sources). The TCA framework further allows to test the features in the data for different statistical relations with an outcome of interest while modeling source-specific effects; particularly, it allows to look for statistical relations between source-specific signals and an outcome. For example, TCA can deconvolve bulk tissue-level DNA methylation data (methylation sites by individuals) into a three-dimensional tensor of cell-type-specific methylation levels for each individual (i.e. methylation sites by individuals by cell types) and it allows to detect cell-type-specific statistical relations (associations) with phenotypes. For more details see Rahmani et al. (2019) <doi:10.1038/s41467-019-11052-9>.

Version: 1.2.1
Depends: R (≥ 3.5.0)
Imports: config, data.table, futile.logger, gmodels, matrixcalc, matrixStats, nloptr, parallel, pbapply, pracma, rsvd, stats, quadprog, Matrix
Suggests: testthat, knitr, rmarkdown
Published: 2021-02-14
Author: Elior Rahmani [aut, cre], Brandon Jew [ctb]
Maintainer: Elior Rahmani <elior.rahmani at gmail.com>
BugReports: https://github.com/cozygene/TCA/issues
License: GPL-3
URL: https://www.nature.com/articles/s41467-019-11052-9
NeedsCompilation: no
Citation: TCA citation info
Materials: README NEWS
CRAN checks: TCA results

Documentation:

Reference manual: TCA.pdf
Vignettes: Detecting differential DNA methylation at cell-type resolution using TCA

Downloads:

Package source: TCA_1.2.1.tar.gz
Windows binaries: r-devel: TCA_1.2.1.zip, r-release: TCA_1.2.1.zip, r-oldrel: TCA_1.2.1.zip
macOS binaries: r-release (arm64): TCA_1.2.1.tgz, r-release (x86_64): TCA_1.2.1.tgz, r-oldrel: TCA_1.2.1.tgz
Old sources: TCA archive

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