sequences: Generic and Biological Sequences
Version 0.5.9

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

AuthorLaurent Gatto [aut, cre], Robert Stojnic [aut]
Bioconductor views DataImport DataRepresentation Infrastructure
Date of publication2014-12-03 13:58:03
MaintainerLaurent Gatto <lg390@cam.ac.uk>
LicenseGPL-3
Version0.5.9
URL https://github.com/lgatto/sequences/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("sequences")

Getting started

Package overview

Popular 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.
sequences-package: A short demo package featuring biological sequences.
See all...

All man pages Function index File listing

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.

Functions

DnaSeq-class Man page
GenericSeq-class Man page
RnaSeq-class Man page
Seq Man page
Seq-class Man page
[,DnaSeq-method Man page
[,GenericSeq-method Man page
[,RnaSeq-method Man page
alphabet Man page
alphabet,DnaSeq-method Man page
alphabet,GenericSeq-method Man page
alphabet,RnaSeq-method Man page
alphabet-method Man page
class:DnaSeq Man page
class:GenericSeq Man page
class:RnaSeq Man page
class:Seq Man page
comp Man page
comp,DnaSeq-method Man page
comp,RnaSeq-method Man page
comp-method Man page
debugme Source code
dnaseq Man page
gccount Man page Source code
gccount2 Man page Source code
id Man page
id,DnaSeq-method Man page
id,GenericSeq-method Man page
id,RnaSeq-method Man page
id-method Man page
id<- Man page
id<-,GenericSeq,ANY-method Man page
id<-,GenericSeq,character-method Man page
length,DnaSeq-method Man page
length,GenericSeq-method Man page
length,RnaSeq-method Man page
onAttach Source code
print,DnaSeq-method Man page
print,GenericSeq-method Man page
print,RnaSeq-method Man page
readFasta Man page Source code
rev Man page
rev,DnaSeq-method Man page
rev,GenericSeq-method Man page
rev,RnaSeq-method Man page
rev-method Man page
seq Man page
seq,DnaSeq-method Man page
seq,GenericSeq-method Man page
seq,RnaSeq-method Man page
seq-method Man page
seq<- Man page
seq<-,GenericSeq,ANY-method Man page
seq<-,GenericSeq,character-method Man page
sequences Man page
sequences-package Man page
show,DnaSeq-method Man page
show,GenericSeq-method Man page
show,RnaSeq-method Man page
transcribe Man page
transcribe,DnaSeq-method Man page
transcribe-method Man page

Files

inst
inst/scripts
inst/scripts/readFasta2.R
inst/extdata
inst/extdata/aDnaSeq.fasta
inst/extdata/moreDnaSeqs.fasta
inst/doc
inst/doc/sequences.Rnw
inst/doc/sequences.R
inst/doc/sequences.pdf
tests
tests/sequences-test.R
tests/testthat.R
tests/testthat
tests/testthat/test_sequences.R
tests/sequences-test.Rout.save
src
src/Makevars
src/gccount2.cpp
src/gccount.c
NAMESPACE
NEWS
data
data/dnaseq.RData
R
R/AllGenerics.R
R/methods-GenSeq.R
R/SeqRefClass.R
R/functions.R
R/methods-DnaSeq.R
R/DataClasses.R
R/methods-RnaSeq.R
R/zzz.R
vignettes
vignettes/sequences.Rnw
vignettes/r-advanced-course-2011.jpg
MD5
build
build/vignette.rds
DESCRIPTION
man
man/dnaseq.Rd
man/Seq-class.Rd
man/sequences-package.Rd
man/readFasta.Rd
man/GenericSeq-class.Rd
man/gccount2.Rd
man/gccount.Rd
man/DnaSeq-class.Rd
sequences documentation built on May 19, 2017, 6:39 p.m.

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