rDNAse: Generating Various Numerical Representation Schemes of DNA Sequences

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

Author
Min-feng Zhu <wind2zhu@163.com>, Jie Dong <biomed@csu.edu.cn>, Dong-sheng Cao <oriental-cds@163.com>
Date of publication
2016-07-14 07:18:52
Maintainer
Min-feng Zhu <wind2zhu@163.com>
License
GPL (>= 2)
Version
1.1-1
URLs

View on CRAN

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

Files in this package

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