ScDeconv: an R package to deconvolve bulk DNA methylation data with scRNA-seq data and paired bulk RNA-DNA methylation data.

ABSTRACT: Many DNA methylation (DNAm) data are from tissues composed of various cell types, and hence cell deconvolution methods are needed to infer their cell compositions accurately. However, a bottleneck for DNAm data is the lack of cell-type-specific DNAm references. On the other hand, scRNA-seq data are being accumulated rapidly with various cell-type transcriptomic signatures characterized, and also, many paired bulk RNA-DNAm data are publicly available currently. Hence, we developed the R package scDeconv to use these resources to solve the reference deficiency problem of DNAm data and deconvolve them from scRNA-seq data in a trans-omics manner. It assumes that paired samples have similar cell compositions. So the cell content information deconvolved from the scRNA-seq and paired RNA data can

SUBMITTER: Liu Y 

PROVIDER: S-EPMC9271220 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature