ADAPTS
Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells
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>.
README
# ADAPTS
Augments existing or de-novo cell-type signature matrices to deconvolve bulk gene expression data This package expands on the techniques outlined in Newman et al.'s 2015 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.
To install this package in R, use devtools.
install.packages('devtools')
library(devtools)
devtools::install_github('sdanzige/ADAPTS')
Data for the Vignette can be found at sdanzige/ADAPTSdata, sdanziger/ADAPTSdata2, sdanziger/ADAPTSdata3 and yxinyi2/ADAPTSdata4
More information about this package is available on bioRxiv (https://www.biorxiv.org/content/10.1101/633958v2) and this package has been officially released as an R package on CRAN (https://cran.r-project.org/web/packages/ADAPTS/).
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
1.0.22 |
rolling linux/jammy R-4.5 | ADAPTS_1.0.22.tar.gz |
4.6 MiB |
1.0.22 |
rolling linux/noble R-4.5 | ADAPTS_1.0.22.tar.gz |
4.6 MiB |
1.0.22 |
rolling source/ R- | ADAPTS_1.0.22.tar.gz |
4.6 MiB |
1.0.22 |
latest linux/jammy R-4.5 | ADAPTS_1.0.22.tar.gz |
4.6 MiB |
1.0.22 |
latest linux/noble R-4.5 | ADAPTS_1.0.22.tar.gz |
4.6 MiB |
1.0.22 |
latest source/ R- | ADAPTS_1.0.22.tar.gz |
4.6 MiB |
1.0.22 |
2026-04-26 source/ R- | ADAPTS_1.0.22.tar.gz |
4.6 MiB |
1.0.22 |
2026-04-23 source/ R- | ADAPTS_1.0.22.tar.gz |
4.6 MiB |
1.0.22 |
2025-04-20 source/ R- | ADAPTS_1.0.22.tar.gz |
4.6 MiB |