Package: BASiNETEntropy 0.99.6
BASiNETEntropy: Classification of RNA Sequences using Complex Network and Information Theory
It makes the creation of networks from sequences of RNA, with this is done the abstraction of characteristics of these networks with a methodology of maximum entropy for the purpose of making a classification between the classes of the sequences. There are two data present in the 'BASiNET' package, "mRNA", and "ncRNA" with 10 sequences. These sequences were taken from the data set used in the article (LI, Aimin; ZHANG, Junying; ZHOU, Zhongyin, 2014) <doi:10.1186/1471-2105-15-311>, these sequences are used to run examples.
Authors:
BASiNETEntropy_0.99.6.tar.gz
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BASiNETEntropy.pdf |BASiNETEntropy.html✨
BASiNETEntropy/json (API)
| # Install 'BASiNETEntropy' in R: |
| install.packages('BASiNETEntropy', repos = c('https://fabriciomlopes.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwarebiologicalquestiongenepredictionfunctionalpredictionnetworkclassification
Last updated 1 years agofrom:a9d9de0d2a. Checks:OK: 6 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 08 2024 |
| R-4.5-win | OK | Nov 08 2024 |
| R-4.5-linux | WARNING | Nov 08 2024 |
| R-4.4-win | OK | Nov 08 2024 |
| R-4.4-mac | OK | Nov 08 2024 |
| R-4.3-win | OK | Nov 08 2024 |
| R-4.3-mac | OK | Nov 08 2024 |
Exports:classifycurveofentropytraining
Dependencies:askpassBiocGenericsBiostringsclicpp11crayoncurlgenericsGenomeInfoDbGenomeInfoDbDatagluehttrigraphIRangesjsonlitelatticelifecyclemagrittrMatrixmimeopensslpkgconfigR6randomForestrlangS4VectorssysUCSC.utilsvctrsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Performs the classification methodology using complex network and entropy theories | classify |
| Creates an untargeted graph from a biological sequence | createedges |
| Creates a feature matrix using complex network topological measures | creatingDataframe |
| Creates an entropy curve | curveofentropy |
| Calculates the entropy | entropy |
| Filters the edges | filtering |
| Compares the matrices | matrixmultiplication |
| Calculates the maximum entropy | maxentropy |
| Rescales the results between values from 0 to 1 | preprocessing |
| Selects the edges of the adjacency matrix | selectingEdges |
| Trains the algorithm to select the edges that maximize the entropy | training |
