Automated Deconvolution Augmentation of Profiles for Tissue
Specific Cells
Augments existing or de-novo cell-type signature matrices to deconvolve bulk gene expression data.
This package expands on the techniques outlined in Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y,
Hoang CD, Diehn M, Alizadeh, AA (2015) <doi:10.1038/nmeth.3337>'s Nature Methods paper:
'Robust enumeration of cell subsets from tissue expression profiles'  to allow a user to easily add
their own cell types (e.g. a tumor specific cell type) to Newman's LM22 or other signature matrix.
missForest, e1071, WGCNA, ComICS, pheatmap, doParallel,
quantmod, preprocessCore, pcaMethods, foreach, DeconRNASeq

Augments existing or de-novo cell-type signature matrices to deconvolve bulk gene expression data.
Useful for building signature matrices from single cell RNAseq data, determine cell type deconvolution
spillover, and hierarchical deconvolution to use spillover to increase deconvolution accuracy. Please cite:
Danziger SA et al. (2019) ADAPTS: Automated Deconvolution Augmentation of Profiles for
Tissue Specific cells <doi:10.1101/633958>. This package expands on the techniques outlined in Newman AM,
Liu CL, Green MR, Gentles AJ, Feng W, Xu Y,
Hoang CD, Diehn M, Alizadeh, AA (2015) <doi:10.1038/nmeth.3337>'s Nature Methods paper:
'Robust enumeration of cell subsets from tissue expression profiles'  to allow a user to easily add
their own cell types (e.g. a tumor specific cell type) to Newman's LM22 or other signature matrix.
missForest, e1071, WGCNA, ComICS, pheatmap, doParallel,
quantmod, preprocessCore, pcaMethods, foreach, DeconRNASeq,
nnls

Tools to construct (or add to) cell-type signature matrices using flow sorted or single cell samples and deconvolve bulk gene expression data.
Useful for assessing the quality of single cell RNAseq experiments, estimating the accuracy of signature matrices, and determining cell-type spillover.
Please cite: Danziger SA et al. (2019) ADAPTS: Automated Deconvolution Augmentation of Profiles for Tissue Specific cells <doi:10.1371/journal.pone.0224693>.
missForest, e1071, ComICS, pheatmap, doParallel, utils,
quantmod, preprocessCore, pcaMethods, foreach, nnls, ranger