DART: Denoising Algorithm based on Relevance network Topology

Package: DART 1.61.0

Charles Shijie Zheng

DART: Denoising Algorithm based on Relevance network Topology

Denoising Algorithm based on Relevance network Topology (DART) is an algorithm designed to evaluate the consistency of prior information molecular signatures (e.g in-vitro perturbation expression signatures) in independent molecular data (e.g gene expression data sets). If consistent, a pruning network strategy is then used to infer the activation status of the molecular signature in individual samples.

Authors:Yan Jiao, Katherine Lawler, Andrew E Teschendorff, Charles Shijie Zheng

DART_1.61.0.tar.gz
DART_1.61.0.zip(r-4.7)DART_1.61.0.zip(r-4.6)DART_1.61.0.zip(r-4.5)
DART_1.61.0.tgz(r-4.6-any)DART_1.61.0.tgz(r-4.5-any)
DART_1.61.0.tar.gz(r-4.7-any)DART_1.61.0.tar.gz(r-4.6-any)
DART_1.61.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DART/json (API)

# Install 'DART' in R:

install.packages('DART', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

dataDART - Example data for DART package

On BioConductor:DART-1.61.0(bioc 3.24)DART-1.60.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpression differentialexpression graphandnetwork pathways

4.30 score 1 scripts 182 mentions 6 exports 11 dependencies

Last updated from:ccc8d18717. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	125
linux-devel-x86_64	NOTE	156
source / vignettes	OK	179
linux-release-x86_64	NOTE	140
macos-release-arm64	NOTE	98
macos-oldrel-arm64	NOTE	90
windows-devel	NOTE	82
windows-release	NOTE	81
windows-oldrel	NOTE	82
wasm-release	OK	109

Exports:BuildRN DoDART DoDARTCLQ EvalConsNet PredActScore PruneNet

Dependencies:cli cpp11 glue igraph lattice lifecycle magrittr Matrix pkgconfig rlang vctrs

DART Tutorial

Rendered fromDART.Rnwusingutils::Sweave

Help page	Topics
Denoising Algorithm based on Relevance network Topology	DART
Builds the relevance correlation network	BuildRN
Example data for DART package	dataDART
Main function of DART	DoDART
Improved edition of DoDART	DoDARTCLQ
Evaluates the consistency of the inferred relevance correlation network with the correlations predicted by the model pathway signature.	EvalConsNet
Computes the DART activation score of the model signature in the samples of a data set.	PredActScore
Prunes relevance network to allow only edges that are consistent with the predictions of the model signature	PruneNet

Help page

Topics

Denoising Algorithm based on Relevance network Topology

DART

Builds the relevance correlation network

BuildRN

Example data for DART package

dataDART

Main function of DART

DoDART

Improved edition of DoDART

DoDARTCLQ