rDNAse (version 1.1-1)

Generating Various Numerical Representation Schemes of DNA Sequences

Description

Comprehensive toolkit for generating various numerical representation schemes of DNA sequence. The descriptors and similarity scores included are extensively used in bioinformatics and chemogenomics.

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Install

install.packages('rDNAse')

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Version

1.1-1

License

GPL (>= 2)

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Repository

https://github.com/wind22zhu/rDNAse

Maintainer

Minfeng Zhu

Last Published

July 14th, 2016

Functions in rDNAse (1.1-1)

extrTCC

The Trinucleotide-based Cross Covariance Descriptor

extrDCC

The Dinucleotide-based Cross Covariance Descriptor

dnacheck

Check if the DNA sequence are in the 4 default types

extrDACC

The Dinucleotide-based Auto-cross Covariance Descriptor

extrTAC

The Trinucleotide-based Auto Covariance Descriptor

diversity

diversity function for make_kmer_vec

extrPseKNC

The Pseudo K-tupler Composition Descriptor

extrDAC

The Dinucleotide-based Auto Covariance Descriptor

extrPseDNC

The Pseudo Dinucleotide Composition Descriptor

extrTACC

The Trinucleotide-based Auto-cross Covariance Descriptor

parSeqSim

Parallellized DNA/RNA Sequence Similarity Calculation based on Sequence Alignment

getGenbank

Get DNA/RNA Sequences from Genbank by GI ID

kmer

The Basic Kmer Descriptor

id_x_s

id_x_s function for make_kmer_vec

twoSeqSim

DNA/RNA Sequence Alignment for Two DNA/RNA Sequences

readFASTA

Read DNA/RNA Sequences in FASTA Format

make_idkmer_vec

The Increment Of Diversity Descriptors

make_kmer_index

Calculate The Basic Kmer Feature Vector