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DESCRIPTION
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DESCRIPTION
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Package: NPA
Type: Package
Title: Network Perturbation Amplitude
Version: 0.99.0
Date: 2020-03-18
Author: Florian Martin <[email protected]>, Sylvain Gubian
Maintainer: Sylvain Gubian <[email protected]>
Depends:
R (>= 3.5),
R6
Imports:
grid,
grDevices,
graphics,
stats,
utils,
ggplot2,
plotrix,
gplots,
RColorBrewer,
RGraph2js,
reshape2,
stringr,
methods,
scales,
graph,
Rgraphviz,
dnet,
igraph,
supraHex,
NPAModels
Description: Scoring method of Biological Networks based on NPA (Network
Perturbation Amplitude) algorithm. The methodology implemented enables
to translate the gene expression fold-changes into differential values
for each network node, and to summarize this at the network level to
provide a quantitative assessment of the degree of perturbation of the
network model, the Network Perturbation Amplitude (NPA).
Combining multiple relevant network models, the overall biological impact
(BIF) of a perturbing agent, the Biological Impact Factor, can be
calculated by aggregating individual NPA scores.
License: file LICENSE
LazyLoad: yes
RoxygenNote: 6.1.1
Collate:
'BIF-class.R'
'COPD1.R'
'utils.R'
'colorscale.R'
'getNPALE.R'
'getNPAmodulesGlobal.R'
'NPA-class.R'
'NPA.R'
'imageplot_gg.R'
'extract_npas.R'
'getBIF.R'
'NPAList-class.R'
'NPAallrename.R'
'NPAheatmap.R'
'NPAsubset.R'
'getNPALEtable2.R'
'as.matrix.R'
'starplot.R'
'barplotBIF.R'
'barplotNPAGG.R'
'barplotNPA.R'
'barplotNPA3.R'
'barplot.R'
'computeNPA.R'
'drawNPAjs.R'
'visNet2.R'
'drawNPAmodule.R'
'getBIF0weighted.R'
'getBIFdist.R'
'getC.R'
'getLE.R'
'getsplit.R'
'getNPAmodules.R'
'getNPAnames.R'
'getNets.R'
'getNets1.R'
'getNets2.R'
'getWeightedBIF.R'
'npa_example.R'
'onLoad.R'
'plotNPAmodulesGlobal.R'
'starplotBIFnetworks.R'
'starplotBIFcontrasts.R'
'plot.R'
'subset.R'
biocViews: DifferentialExpression, Visualization, Network, GraphAndNetwork, MathematicalBiology, SystemsBiology, Transcriptomics, GeneExpression
Suggests:
knitr,
rmarkdown,
testthat
VignetteBuilder: knitr