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.
| Version: | 1.0.3 |
| Depends: | R (≥ 3.3.0) |
| Imports: | missForest, e1071, WGCNA, ComICS, pheatmap, doParallel, quantmod, preprocessCore, pcaMethods, foreach, DeconRNASeq, nnls, ranger |
| Suggests: | R.rsp |
| Published: | 2020-08-05 |
| Author: | Samuel A Danziger |
| Maintainer: | Samuel A Danziger <sam.danziger at gmail.com> |
| License: | MIT + file LICENSE |
| Copyright: | Celgene Corporation |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | ADAPTS results |
| Reference manual: | ADAPTS.pdf |
| Vignettes: |
ADAPTS (Automated Deconvolution Augmentation of Profiles for Tissue Specific cells) Vignette ADAPTS Vignette #2: Single Cell Analysis ADAPTS Vignette #3 ADAPTS Vignette #4 |
| Package source: | ADAPTS_1.0.3.tar.gz |
| Windows binaries: | r-devel: ADAPTS_1.0.3.zip, r-release: ADAPTS_1.0.3.zip, r-oldrel: ADAPTS_0.9.26.zip |
| macOS binaries: | r-release: not available, r-oldrel: not available |
| Old sources: | ADAPTS archive |
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