Package: ADAPTS
Type: Package
Title: Automated Deconvolution Augmentation of Profiles for Tissue
        Specific Cells
Version: 0.9.26
Author: Samuel A Danziger
Maintainer: Samuel A Danziger <sam.danziger@gmail.com>
Copyright: Celgene Corporation
Description: 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. 
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: R (>= 3.3.0)
biocViews:
Imports: missForest, e1071, WGCNA, ComICS, pheatmap, doParallel,
        quantmod, preprocessCore, pcaMethods, foreach, DeconRNASeq,
        nnls
Suggests: R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2019-10-28 23:07:44 UTC; sdanziger
Repository: CRAN
Date/Publication: 2019-10-29 05:10:02 UTC
Built: R 3.5.3; ; 2020-04-22 09:39:31 UTC; windows
