Generic and Biological Sequences

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


News

CHANGES IN VERSION 0.5.9

o fasta file with 3 sequences in extdata and fun to debug in inst/scripts [2014-11-01 Sat] o use knitr for vignette [2014-11-01 Sat] o fix duplicated sequence name in fasta file (pull request by Julian Gehring) [2014-11-09 Sun] o Title: Use title case and remove period [2014-12-03 Wed] o fix readFasta example and test to use first file [2014-12-03 Wed]

CHANGES IN VERSION 0.5.8

o update to testthat 0.8 [2014-03-14 Fri]

CHANGES IN VERSION 0.5.7

o better gccount2.cpp <2013-05-17 Fri> o test that gccount c/cpp/r produces identical results <2013-05-17 Fri>

CHANGES IN VERSION 0.5.6

o updated gccount2.cpp <2013-05-15 Wed> o typo Author[s]@R <2013-05-15 Wed> o using ./vignettes <2013-05-15 Wed> o added URL <2013-05-16 Thu>

CHANGES IN VERSION 0.5.5

o updated gccount.c <2013-05-15 Wed> o updates Description of package <2013-05-15 Wed>

CHANGES IN VERSION 0.5.4

o added seqinr package reference in vignette <2012-02-10 Fri>

CHANGES IN VERSION 0.5.3

o updated vignette with course background <2012-01-07 Sat> o udded biocViews to DESCRIPTION <2012-01-07 Sat>

CHANGES IN VERSION 0.5.2

o added Cpp example

CHANGES IN VERSION 0.5.1

o added figure example in vignette <2011-11-24 Thu> o updated inst/doc/Makefile to build vignette <2011-11-24 Thu>

CHANGES IN VERSION 0.5.0

o added Seq reference class <2011-11-23 Wed> o Seq documentation <2011-11-23 Wed>

CHANGES IN VERSION 0.4.1

o added [,GenSeq-method

CHANGES IN VERSION 0.4.0

o created test_that tests

CHANGES IN VERSION 0.3.9

o added startup message o defined "$(R_HOME)/bin/R" in inst/doc/Makefile

CHANGES IN VERSION 0.3.8

o fixed type in DnaSeq-class.Rd o added rev alias to GenericSeq-class o added -method aliases

CHANGES IN VERSION 0.3.7

o added gccount.c code

CHANGES IN VERSION 0.3.6

o update print method, remove pgfSweave dependency for vignette and added print exemple chunk

CHANGES IN VERSION 0.3.5

o added toupper in seq replaceMethod

CHANGES IN VERSION 0.3.4

o added tests

CHANGES IN VERSION 0.3.3

o added initialize method for GenericSeq

CHANGES IN VERSION 0.3.2

o added LazyData

CHANGES IN VERSION 0.3.1

o Added NEWS file

CHANGES IN VERSION 0.3

o Code and man completed - checks without warnings

Reference manual

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install.packages("sequences")

0.5.9 by Laurent Gatto, 4 years ago


https://github.com/lgatto/sequences/


Browse source code at https://github.com/cran/sequences


Authors: Laurent Gatto [aut, cre] , Robert Stojnic [aut]


Documentation:   PDF Manual  


GPL-3 license


Depends on methods, Rcpp

Suggests testthat, knitr

Linking to Rcpp


See at CRAN