sequences: Generic and Biological Sequences

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Educational package used in R courses to illustrate object-oriented programming and package development. Using biological sequences (DNA and RNA) as a working example.

Author
Laurent Gatto [aut, cre], Robert Stojnic [aut]
Date of publication
2014-12-03 13:58:03
Maintainer
Laurent Gatto <lg390@cam.ac.uk>
License
GPL-3
Version
0.5.9
URLs

View on CRAN

Man pages

dnaseq
An 'DnaSeq' example.
DnaSeq-class
Class "DnaSeq" and "RnaSeq"
gccount
Count bases in sequence
gccount2
Count bases in sequence (using Rcpp)
GenericSeq-class
Class "GenericSeq"
readFasta
Read fasta files.
Seq-class
Class '"Seq"'
sequences-package
A short demo package featuring biological sequences.

Files in this package

sequences
sequences/inst
sequences/inst/scripts
sequences/inst/scripts/readFasta2.R
sequences/inst/extdata
sequences/inst/extdata/aDnaSeq.fasta
sequences/inst/extdata/moreDnaSeqs.fasta
sequences/inst/doc
sequences/inst/doc/sequences.Rnw
sequences/inst/doc/sequences.R
sequences/inst/doc/sequences.pdf
sequences/tests
sequences/tests/sequences-test.R
sequences/tests/testthat.R
sequences/tests/testthat
sequences/tests/testthat/test_sequences.R
sequences/tests/sequences-test.Rout.save
sequences/src
sequences/src/Makevars
sequences/src/gccount2.cpp
sequences/src/gccount.c
sequences/NAMESPACE
sequences/NEWS
sequences/data
sequences/data/dnaseq.RData
sequences/R
sequences/R/AllGenerics.R
sequences/R/methods-GenSeq.R
sequences/R/SeqRefClass.R
sequences/R/functions.R
sequences/R/methods-DnaSeq.R
sequences/R/DataClasses.R
sequences/R/methods-RnaSeq.R
sequences/R/zzz.R
sequences/vignettes
sequences/vignettes/sequences.Rnw
sequences/vignettes/r-advanced-course-2011.jpg
sequences/MD5
sequences/build
sequences/build/vignette.rds
sequences/DESCRIPTION
sequences/man
sequences/man/dnaseq.Rd
sequences/man/Seq-class.Rd
sequences/man/sequences-package.Rd
sequences/man/readFasta.Rd
sequences/man/GenericSeq-class.Rd
sequences/man/gccount2.Rd
sequences/man/gccount.Rd
sequences/man/DnaSeq-class.Rd