Package: EncDNA 1.0.2

EncDNA: Encoding of Nucleotide Sequences into Numeric Feature Vectors

We describe fifteen different splice site sequence encoding schemes that have been used in earlier studies for mapping of splice site sequences into numeric feature vectors. These encoding schemes will also be helpful for transforming other nucleotide sequences into numeric forms, provided they are of equal length. These encoding schemes will help the computational biologist working in the field of classification (binary or multiclass) or prediction involving nucleic acid sequences of equal length.

Authors:Prabina Kumar Meher

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EncDNA.pdf |EncDNA.html✨
EncDNA/json (API)

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

Peer review:

Datasets:
  • droso - An example dataset consisting of true and false donor splice sites of Drosophila melanogaster.

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

15 exports 1 stars 0.09 score 18 dependencies 160 downloads

Last updated 5 years agofrom:621ffb4eff. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 15 2024
R-4.5-winNOTESep 15 2024
R-4.5-linuxNOTESep 15 2024
R-4.4-winNOTESep 15 2024
R-4.4-macNOTESep 15 2024
R-4.3-winOKSep 15 2024
R-4.3-macOKSep 15 2024

Exports:APR.FeatureBayes.FeatureDensity.FeatureMaldoss.FeatureMM1.FeatureMM2.FeatureMN.Fdtf.FeaturePN.Fdtf.FeaturePOS.FeaturePredoss.FeatureSAE.FeatureSparse.FeatureTrint.Dist.FeatureWAM.FeatureWMM.Feature

Dependencies:askpassBiocGenericsBiostringscrayoncurlGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utilsXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Adjacent position relationship feature.APR.Feature
Projecting nucleotide sequences into numeric feature vectors using Bayes kernel encoding approach.Bayes.Feature
Nucleotide sequence encoding with the distribution of trinucleotides.Density.Feature
An example dataset consisting of true and false donor splice sites of Drosophila melanogaster.droso
Encoding of nucleic acid sequences using di-nucleotide frequency difference between positive and negative class datasets.Maldoss.Feature
Transforming nucleotide sequences into numeric vectors using first order nucleotide dependency.MM1.Feature
Mapping nucleotide sequences onto numeric feature vectors based on second order nucleotide dependencies.MM2.Feature
Sequence encoding with nucleotide frequency difference between two classes of sequence datasets.MN.Fdtf.Feature
Conversion of nucleotide sequences into numeric feature vectors based on the difference of dinucleotide frequency.PN.Fdtf.Feature
Transformation of nucleic acid sequences into numeric vectors using position-wise frequency of nucleotides.POS.Feature
Encoding nucleotide sequences using all possible di-nucleotide dependencies.Predoss.Feature
Encoding of nucleotide sequences based on sum of absolute error (SAE) of each sequence.SAE.Feature
Nucleotide sequence encoding with 0 and 1.Sparse.Feature
Tri-nucleotide distribution-based encoding of nucleotide sequences.Trint.Dist.Feature
Nucleic acid sequence encoding based on weighted array model.WAM.Feature
Weighted matrix model based mapping of nucleotide sequences into vectors of numeric observations.WMM.Feature