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>.

Last updated 4 years ago

7.25 score 17 stars 2 packages 35 scripts 274 downloads

BisqueRNA - Decomposition of Bulk Expression with Single-Cell Sequencing

Provides tools to accurately estimate cell type abundances from heterogeneous bulk expression. A reference-based method utilizes single-cell information to generate a signature matrix and transformation of bulk expression for accurate regression based estimates. A marker-based method utilizes known cell-specific marker genes to measure relative abundances across samples. For more details, see Jew and Alvarez et al (2019) <doi:10.1101/669911>.

Last updated 4 years ago

6.92 score 68 stars 123 scripts 773 downloads

Unico - Unified Cross-Omics Deconvolution

UNIfied Cross-Omics deconvolution (Unico) deconvolves standard 2-dimensional bulk matrices of samples by features into a 3-dimensional tensors representing samples by features by cell types. Unico stands out as the first principled model-based deconvolution method that is theoretically justified for any heterogeneous genomic data. For more details see Chen and Rahmani et al. (2024) <doi:10.1101/2024.01.27.577588>.

Last updated 9 months ago

4.40 score 1 stars 5 scripts 202 downloads