Abstract
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 uniquely 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, ADAPTSdata2 are at GitHub (https://github.com/sdanzige/ADAPTS, etc.) and eventually will be available on CRAN
Contact sdanziger{at}celgene.com, aratushny{at}celgene.com
Preprint A preprint is available on BiorXiv (www.biorxiv.org/content/10.1101/633958v1)
Footnotes
This version points to the GitHub version of the code to use while the CRAN submission is pending.
