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>.
| Version: | 1.0.6 |
| Depends: | R (≥ 3.3.0) |
| Imports: | missForest, e1071, WGCNA, ComICS, pheatmap, doParallel, quantmod, preprocessCore, pcaMethods, foreach, nnls, ranger |
| Suggests: | R.rsp, DeconRNASeq |
| Published: | 2020-10-17 |
| Author: | Samuel A Danziger |
| Maintainer: | Samuel A Danziger <sam.danziger at gmail.com> |
| License: | MIT + file LICENSE |
| Copyright: | Bristol-Myers Squibb |
| 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: (DEPRECATED) Single Cell Analysis ADAPTS Vignette #3: Building a Better Signature Matrix From Single Cell Data ADAPTS Vignette #4: Build a Single Cell Based Matrix and Test on Independant Data ADAPTS Vignette #5: Repeated Leave-Half-Out Cross-Validation for Robust Accuracy Estimates |
| Package source: | ADAPTS_1.0.6.tar.gz |
| Windows binaries: | r-devel: ADAPTS_1.0.6.zip, r-release: ADAPTS_1.0.6.zip, r-oldrel: ADAPTS_1.0.6.zip |
| macOS binaries: | r-release: not available, r-oldrel: not available |
| Old sources: | ADAPTS archive |
| Reverse imports: | scMappR |
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