2022
DOI: 10.1093/bioinformatics/btac262
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Semi-deconvolution of bulk and single-cell RNA-seq data with application to metastatic progression in breast cancer

Abstract: Motivation Identifying cell types and their abundances and how these evolve during tumor progression is critical to understanding the mechanisms of metastasis and identifying predictors of metastatic potential that can guide the development of new diagnostics or therapeutics. Single-cell RNA sequencing (scRNA-seq) has been especially promising in resolving heterogeneity of expression programs at the single-cell level, but is not always feasible, e.g. for large cohort studies or longitudinal a… Show more

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“…Complete algorithms return both and . Here we selected nine deconvolution algorithms: DeconRNASeq [ 12 ], lsfit [ 31 ], DWLS [ 14 ], NMF [ 3 ], two versions of deconf (original and fast) [ 32 , 33 ], bMIND [ 34 ], RADs [ 35 ], and Scaden [ 36 ]. Scaden was a supervised deep learning algorithm that required labels of sc-RNASeq data, hence was not applicable for our cancer datasets due to lack of cancer cell type annotations.…”
Section: Methodsmentioning
confidence: 99%
“…Complete algorithms return both and . Here we selected nine deconvolution algorithms: DeconRNASeq [ 12 ], lsfit [ 31 ], DWLS [ 14 ], NMF [ 3 ], two versions of deconf (original and fast) [ 32 , 33 ], bMIND [ 34 ], RADs [ 35 ], and Scaden [ 36 ]. Scaden was a supervised deep learning algorithm that required labels of sc-RNASeq data, hence was not applicable for our cancer datasets due to lack of cancer cell type annotations.…”
Section: Methodsmentioning
confidence: 99%