CRAN/E | ADAPTS

Installation

About

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.

Copyright

Bristol-Myers Squibb

Key Metrics

Version	1.0.22
R	≥ 3.3.0
Published	2022-09-14 589 days ago
Needs compilation?	no
License	MIT
License	File
CRAN checks	ADAPTS results

Downloads

Yesterday	35 +192%
Last 7 days	107 -4%
Last 30 days	437 -3%
Last 90 days	1.257 -11%
Last 365 days	5.324 -2%

Maintainer

Samuel A Danziger

sam.danziger@gmail.com

Authors

Samuel A Danziger

Material

README
Reference manual
Package source

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: Automated Repeated Leave-Half-Out Cross-Validation for Robust Accuracy Estimates

macOS

r-release	arm64
r-oldrel	arm64
r-release	x86_64
r-oldrel	x86_64

Windows

r-devel	x86_64
r-release	x86_64
r-oldrel	x86_64

Old Sources

ADAPTS archive

Depends

R

≥ 3.3.0

Imports

missForest
e1071
ComICS
pheatmap
doParallel
utils
quantmod
preprocessCore
pcaMethods
foreach
nnls
ranger

Suggests

R.rsp
DeconRNASeq
WGCNA

Reverse Imports

scMappR

ADAPTS

Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells