Package: Cascade 2.1

Cascade: Selection, Reverse-Engineering and Prediction in Cascade Networks

A modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.

Authors:Frederic Bertrand [cre, aut], Myriam Maumy-Bertrand [aut], Laurent Vallat [ctb], Nicolas Jung [ctb]

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Cascade.pdf |Cascade.html✨
Cascade/json (API)
NEWS

# Install 'Cascade' in R:
install.packages('Cascade', repos = c('https://fbertran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/fbertran/cascade/issues

Datasets:
  • M - Simulated M data for examples.
  • Net - Simulated network data for examples.
  • Net_inf - Reverse-engineered network of the simulated data.
  • Selection - Selection of genes.
  • network - A network object data.

On CRAN:

18 exports 1 stars 5.35 score 25 dependencies 2 dependents 64 mentions 62 scripts 401 downloads

Last updated 2 years agofrom:ee741407bb. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 18 2024
R-4.5-winOKSep 18 2024
R-4.5-linuxOKSep 18 2024
R-4.4-winOKSep 18 2024
R-4.4-macOKSep 18 2024
R-4.3-winOKSep 18 2024
R-4.3-macOKSep 18 2024

Exports:analyze_networkas.micro_arraycomparecutoffevolutiongene_expr_simulationgeneNeighborhoodgenePeakSelectiongeneSelectionheadinferencenetwork_randomplotpositionpredictprintsummaryunionMicro

Dependencies:abindanimationcliclustercpp11curlglueigraphlarslatticelifecyclelimmamagicmagickmagrittrMatrixnnlspkgconfigRcpprlangstatmodsurvivaltnetvctrsVGAM

Cascade: E-MTAB-1475_re-analysis

Rendered fromE-MTAB-1475_re-analysis.pdf.asisusingR.rsp::asison Sep 18 2024.

Last update: 2019-01-27
Started: 2019-01-27

Cascade: Introduction to Cascade

Rendered fromCascade.pdf.asisusingR.rsp::asison Sep 18 2024.

Last update: 2019-01-27
Started: 2019-01-27

Cascade: Manual

Rendered fromCascade-manual.pdf.asisusingR.rsp::asison Sep 18 2024.

Last update: 2019-01-27
Started: 2019-01-27

Readme and manuals

Help Manual

Help pageTopics
The Cascade Package: Selection, Reverse-Engineering and Prediction in Cascade NetworksCascade-package Cascade
Analysing the networkanalyze_network analyze_network,network-method analyze_network-methods
Coerce a matrix into a micro_array object.as.micro_array
Some basic criteria of comparison between actual and inferred network.compare compare,network,network,numeric-method compare-methods
Choose the best cutoffcutoff cutoff,network-method cutoff-methods
Dimension of the datadim dim,micro_array-method dim-methods
See the evolution of the network with change of cutoffevolution evolution,network-method evolution-methods
Simulates microarray data based on a given network.gene_expr_simulation gene_expr_simulation,network-method gene_expr_simulation-methods
Find the neighborhood of a set of nodes.geneNeighborhood geneNeighborhood,network-method geneNeighborhood-methods
Methods for selecting genesgenePeakSelection genePeakSelection,micro_array,numeric-method genePeakSelection-methods geneSelection geneSelection,list,list,numeric-method geneSelection,micro_array,micro_array,numeric-method geneSelection-methods
Overview of a micro_array objecthead,ANY-method head,micro_array-method head-methods methods
Reverse-engineer the networkinference inference,micro_array-method inference-methods
Simulated M data for examples.M
Class '"micro_array"'micro_array-class
Class '"micropredict"'micropredict-class
Simulated network data for examples.Net
Reverse-engineered network of the simulated data.Net_inf
A network object data.network
Generates a network.network_random
Class '"network"'network-class
Plotplot,ANY,ANY-method plot,micropredict,ANY-method plot,micro_array,ANY-method plot,network,ANY-method plot-methods
Returns the position of edges in the networkposition position,network-method position-methods
Prediction of the gene expressions after a knock-out experience 'predict'predict predict,ANY-method predict,micro_array-method predict-methods
Methods for Function 'print'print,ANY-method print,micro_array-method print,network-method print-methods
Selection of genes.Selection
Methods for Function 'summary'summary,ANY-method summary,micro_array-method summary-methods
Makes the union between two micro_array objects.unionMicro unionMicro,list,ANY-method unionMicro,micro_array,micro_array-method unionMicro-methods