BarcodingR: Species Identification using DNA Barcodes

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To perform species identification using DNA barcodes.

Author
Ai-bing ZHANG [aut, cre], Meng-di HAO [aut], Cai-qing YANG [aut], Zhi-yong SHI [aut]
Date of publication
2016-10-18 23:10:36
Maintainer
Ai-bing ZHANG <Zhangab2008@mail.cnu.edu.cn>
License
GPL-2
Version
1.0-2

View on CRAN

Man pages

barcodes.eval
Barcodes Evaluation
barcoding.gap
Barcoding Gap Calculation
barcoding.spe.identify
Species Identification using Protein-coding Barcodes
barcoding.spe.identify2
Species Identification Based on Fuzzy-set Method and kmer
bbsik
Bp Barcoding Species Identify using Kmer
char2NumVector
Character to Integer Vector
compare2delimitations
Comparision between two Delimitations
consensus.identify
Consensus Identification
digitize.DNA
Digitize DNAbin
DNAbin2kmerFreqMatrix
Calculation of Kmer Frequency Matrix from DNAbin for Both...
FMF
Fuzzy Membership Function Value
FMFtheta12
Calculate Intraspecific and Interspecific Variation
NAMES
Extracts Lables of Samples
optimize.kmer
Optimize kmer Length
pineMothCOI
pine Moth COI
pineMothITS1
pine Moth ITS1
pineMothITS2
pine Moth ITS2
sample.ref
Sample Random Datasets from References (DNAbin)
save.ids
Save Identifications
summarize.ref
Summarize Reference Data
TDR2
TDR2 Species Membership Value
TibetanMoth
Tibetan Moth

Files in this package

BarcodingR
BarcodingR/NAMESPACE
BarcodingR/data
BarcodingR/data/pineMothITS2.rda
BarcodingR/data/pineMothCOI.rda
BarcodingR/data/pineMothITS1.rda
BarcodingR/data/TibetanMoth.rda
BarcodingR/R
BarcodingR/R/FMFtheta12.R
BarcodingR/R/DNAbin2kmerFreqMatrix.R
BarcodingR/R/TDR2.R
BarcodingR/R/char2NumVector.R
BarcodingR/R/consensus.identify.R
BarcodingR/R/digitize.DNA.R
BarcodingR/R/bbsik.R
BarcodingR/R/NAMES.R
BarcodingR/R/barcoding.gap.R
BarcodingR/R/FMF.R
BarcodingR/R/sample.ref.R
BarcodingR/R/save.ids.R
BarcodingR/R/compare2delimitations.R
BarcodingR/R/barcoding.spe.identify2.R
BarcodingR/R/optimize.kmer.R
BarcodingR/R/summarize.ref.R
BarcodingR/R/barcodes.eval.R
BarcodingR/R/barcoding.spe.identify.R
BarcodingR/MD5
BarcodingR/DESCRIPTION
BarcodingR/man
BarcodingR/man/save.ids.Rd
BarcodingR/man/consensus.identify.Rd
BarcodingR/man/compare2delimitations.Rd
BarcodingR/man/DNAbin2kmerFreqMatrix.Rd
BarcodingR/man/optimize.kmer.Rd
BarcodingR/man/TDR2.Rd
BarcodingR/man/barcoding.spe.identify2.Rd
BarcodingR/man/summarize.ref.Rd
BarcodingR/man/barcoding.gap.Rd
BarcodingR/man/digitize.DNA.Rd
BarcodingR/man/FMFtheta12.Rd
BarcodingR/man/NAMES.Rd
BarcodingR/man/pineMothITS1.Rd
BarcodingR/man/pineMothITS2.Rd
BarcodingR/man/sample.ref.Rd
BarcodingR/man/barcoding.spe.identify.Rd
BarcodingR/man/FMF.Rd
BarcodingR/man/bbsik.Rd
BarcodingR/man/barcodes.eval.Rd
BarcodingR/man/pineMothCOI.Rd
BarcodingR/man/TibetanMoth.Rd
BarcodingR/man/char2NumVector.Rd