ADAPTS: Automated Deconvolution Augmentation of Profiles for Tissue Specific cells [article]

Samuel Anthony Danziger, David L Gibbs, Ilya Shmulevich, Mark McConnell, Matthew WB Trotter, Frank Schmitz, David J Reiss, Alexander V Ratushny
2019 bioRxiv   pre-print
Summary: Immune cell infiltration of tumors can be an important component for determining patient outcomes, e.g. by inferring immune cell presence by deconvolving gene expression data drawn from a heterogenous mix of cell types. ADAPTS aids deconvolution by adding custom cell types to existing cell- type signature matrices or building new matrices de novo. This R package builds a custom signature matrix from purified cell type gene expression data by automatically determining genes that
more » ... identify each cell type. The package includes functions that call deconvolution algorithms which use the custom signature matrix to estimate the proportion of cell types present in heterogenous samples. Availability: The R packages ADAPTS, ADAPTSdata, and an instructional vignette are available on CRAN.
doi:10.1101/633958 fatcat:s7a6vsrvvrf7jklkt3vzac5me4