Package: Cascade 2.4

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]

Cascade_2.4.tar.gz
Cascade_2.4.zip(r-4.7)Cascade_2.4.zip(r-4.6)Cascade_2.4.zip(r-4.5)
Cascade_2.4.tgz(r-4.6-any)Cascade_2.4.tgz(r-4.5-any)
Cascade_2.4.tar.gz(r-4.7-any)Cascade_2.4.tar.gz(r-4.6-any)
Cascade_2.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Cascade/json (API)
NEWS

# Install 'Cascade' in R:

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

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

Pkgdown/docs site:https://fbertran.github.io

Datasets:

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

On CRAN:

7.44 score 1 stars 4 packages 46 scripts 687 downloads 64 mentions 18 exports 24 dependencies

Last updated from:6e4baa196f. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	201
source / vignettes	OK	247
linux-release-x86_64	OK	182
macos-release-arm64	OK	126
macos-oldrel-arm64	OK	136
windows-devel	OK	521
windows-release	OK	125
windows-oldrel	OK	353
wasm-release	OK	147

Exports:analyze_network as.micro_array compare cutoff evolution gene_expr_simulation geneNeighborhood genePeakSelection geneSelection head inference network_random plot position predict print summary unionMicro

Dependencies:abind animation cli cluster cpp11 curl glue igraph lars lattice lifecycle limma magick magrittr Matrix nnls pkgconfig Rcpp rlang statmod survival tnet vctrs VGAM

Cascade: Introduction to Cascade

Rendered fromCascade.pdf.asisusingR.rsp::asison May 30 2026.

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

Cascade: Manual

Rendered fromCascade-manual.pdf.asisusingR.rsp::asison May 30 2026.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Analysing the network	analyze_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 cutoff	cutoff cutoff,network-method cutoff-methods
Dimension of the data	dim dim,micro_array-method dim-methods
See the evolution of the network with change of cutoff	evolution 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 genes	genePeakSelection 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 object	head,ANY-method head,micro_array-method head-methods methods
Reverse-engineer the network	inference 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
Plot	plot,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 network	position 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