rDNAse: Generating Various Numerical Representation Schemes of DNA Sequences
Version 1.1-1

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

Browse man pages Browse package API and functions Browse package files

AuthorMin-feng Zhu <wind2zhu@163.com>, Jie Dong <biomed@csu.edu.cn>, Dong-sheng Cao <oriental-cds@163.com>
Date of publication2016-07-14 07:18:52
MaintainerMin-feng Zhu <wind2zhu@163.com>
LicenseGPL (>= 2)
Version1.1-1
URL https://github.com/wind22zhu/rDNAse
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rDNAse")

Man pages

diversity: diversity function for make_kmer_vec
dnacheck: Check if the DNA sequence are in the 4 default types
extrDAC: The Dinucleotide-based Auto Covariance Descriptor
extrDACC: The Dinucleotide-based Auto-cross Covariance Descriptor
extrDCC: The Dinucleotide-based Cross Covariance Descriptor
extrPseDNC: The Pseudo Dinucleotide Composition Descriptor
extrPseKNC: The Pseudo K-tupler Composition Descriptor
extrTAC: The Trinucleotide-based Auto Covariance Descriptor
extrTACC: The Trinucleotide-based Auto-cross Covariance Descriptor
extrTCC: The Trinucleotide-based Cross Covariance Descriptor
getGenbank: Get DNA/RNA Sequences from Genbank by GI ID
id_x_s: id_x_s function for make_kmer_vec
kmer: The Basic Kmer Descriptor
make_idkmer_vec: The Increment Of Diversity Descriptors
make_kmer_index: Calculate The Basic Kmer Feature Vector
parGOSim: DNA Sequence Similarity Calculation based on Gene Ontology...
parSeqSim: Parallellized DNA/RNA Sequence Similarity Calculation based...
readFASTA: Read DNA/RNA Sequences in FASTA Format
revchars: The Reverse chars
twoGOSim: DNA Similarity Calculation based on Gene Ontology (GO)...
twoSeqSim: DNA/RNA Sequence Alignment for Two DNA/RNA Sequences

Functions

IncDiv Man page
diversity Man page Source code
dnacheck Man page Source code
extrDAC Man page Source code
extrDACC Man page Source code
extrDCC Man page Source code
extrPseDNC Man page Source code
extrPseKNC Man page Source code
extrTAC Man page Source code
extrTACC Man page Source code
extrTCC Man page Source code
getGenbank Man page Source code
goPairSim Source code
id_x_s Man page Source code
kmer Man page Source code
make_idkmer_vec Man page Source code
make_kmer_index Man page Source code
parGOSim Man page Source code
parSeqSim Man page Source code
readFASTA Man page Source code
revchars Man page Source code
seqPairSim Source code
twoGOSim Man page Source code
twoSeqSim Man page Source code

Files

inst
inst/dnaseq
inst/dnaseq/H_sapiens_pos.fasta
inst/dnaseq/coldspots.fasta
inst/dnaseq/neg.fasta
inst/dnaseq/hotspots.fasta
inst/dnaseq/non-hs.fasta
inst/dnaseq/hs.fasta
inst/dnaseq/H_sapiens_neg.fasta
inst/dnaseq/pos.fasta
inst/sysdata
inst/sysdata/12_trinucleotide_physicochemical_indices.csv
inst/sysdata/6_dinucleotide_physicochemical_indices.csv
inst/sysdata/38_dinucleotide_physicochemical_indices.csv
inst/doc
inst/doc/rDNAse.Rnw
inst/doc/rDNAse.pdf
inst/doc/rDNAse.R
NAMESPACE
R
R/extrPseKNC.R
R/extrPseDNC.R
R/extrDCC.R
R/extrDACC.R
R/extrDAC.R
R/dnacheck.R
R/extrTAC.R
R/parSeqSim.R
R/extrTACC.R
R/extrTCC.R
R/make_kmer_index.R
R/IncDiv.R
R/parGOSim.R
R/readFASTA.R
R/kmer.R
R/revchars.R
R/getGenbank.R
vignettes
vignettes/rDNAse.Rnw
vignettes/fig
vignettes/fig/roc.pdf
vignettes/fig/logo-panel-text.pdf
vignettes/rDNAse.bib
MD5
build
build/vignette.rds
DESCRIPTION
man
man/make_kmer_index.Rd
man/parSeqSim.Rd
man/parGOSim.Rd
man/extrTCC.Rd
man/make_idkmer_vec.Rd
man/extrDCC.Rd
man/diversity.Rd
man/extrPseDNC.Rd
man/extrDAC.Rd
man/readFASTA.Rd
man/extrDACC.Rd
man/id_x_s.Rd
man/getGenbank.Rd
man/twoSeqSim.Rd
man/dnacheck.Rd
man/twoGOSim.Rd
man/revchars.Rd
man/extrTACC.Rd
man/extrTAC.Rd
man/extrPseKNC.Rd
man/kmer.Rd
rDNAse documentation built on May 19, 2017, 3:20 p.m.