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:
Cascade_2.1.tar.gz
Cascade_2.1.zip(r-4.5)Cascade_2.1.zip(r-4.4)Cascade_2.1.zip(r-4.3)
Cascade_2.1.tgz(r-4.4-any)Cascade_2.1.tgz(r-4.3-any)
Cascade_2.1.tar.gz(r-4.5-noble)Cascade_2.1.tar.gz(r-4.4-noble)
Cascade_2.1.tgz(r-4.4-emscripten)Cascade_2.1.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/fbertran/cascade/issues
Last updated 2 years agofrom:ee741407bb. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 17 2024 |
| R-4.5-win | OK | Nov 17 2024 |
| R-4.5-linux | OK | Nov 17 2024 |
| R-4.4-win | OK | Nov 17 2024 |
| R-4.4-mac | OK | Nov 17 2024 |
| R-4.3-win | OK | Nov 17 2024 |
| R-4.3-mac | OK | Nov 17 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 Nov 17 2024.Last update: 2019-01-27
Started: 2019-01-27
Cascade: Introduction to Cascade
Rendered fromCascade.pdf.asisusingR.rsp::asison Nov 17 2024.Last update: 2019-01-27
Started: 2019-01-27
Cascade: Manual
Rendered fromCascade-manual.pdf.asisusingR.rsp::asison Nov 17 2024.Last update: 2019-01-27
Started: 2019-01-27
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The Cascade Package: Selection, Reverse-Engineering and Prediction in Cascade Networks | Cascade-package Cascade |
| 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 |
