diff --git a/DESCRIPTION b/DESCRIPTION index 0a4fffe..28facda 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: seqinr Title: Biological Sequences Retrieval and Analysis -Version: 4.2-43 +Version: 4.2-44 Depends: R (>= 2.10.0) Imports: ade4,segmented Authors@R: c(person("Delphine", "Charif", role = "aut"), diff --git a/man/EXP.Rd b/man/EXP.Rd index 18f8de7..ddb8e63 100644 --- a/man/EXP.Rd +++ b/man/EXP.Rd @@ -53,10 +53,6 @@ or \code{sum( freq * EXP$A3 )}. To do the same with the \%*\% operator you have to explicit the recycling rule as in \code{ drop( freq \%*\% rep(EXP$A, 16))}. } -\source{ -ANALSEQ EXPFILEs for command EXP.\cr -\url{http://pbil.univ-lyon1.fr/software/doclogi/docanals/manuel.html} -} \references{ \code{citation("seqinr")} \describe{ diff --git a/man/amb.Rd b/man/amb.Rd index 0f48936..e2210e4 100644 --- a/man/amb.Rd +++ b/man/amb.Rd @@ -26,7 +26,7 @@ a vector with expanded symbols. \references{ The nomenclature for incompletely specified bases in nucleic acid sequences -at: \url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC341218/} +at: \url{https://pmc.ncbi.nlm.nih.gov/articles/PMC341218/} \code{citation("seqinr")} } diff --git a/man/bma.Rd b/man/bma.Rd index b6cf48f..a3c4b3c 100644 --- a/man/bma.Rd +++ b/man/bma.Rd @@ -23,7 +23,7 @@ bma(nucl, warn.non.IUPAC = TRUE, type = c("DNA", "RNA")) \references{ The nomenclature for incompletely specified bases in nucleic acid sequences -at: \url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC341218/} +at: \url{https://pmc.ncbi.nlm.nih.gov/articles/PMC341218/} \code{citation("seqinr")} } diff --git a/man/oriloc.Rd b/man/oriloc.Rd index 2adeae3..ef1d261 100644 --- a/man/oriloc.Rd +++ b/man/oriloc.Rd @@ -65,13 +65,6 @@ skew in third codon positions. } \references{ -More illustrated explanations to help understand oriloc outputs -are available there: -\url{https://pbil.univ-lyon1.fr/software/Oriloc/howto.html}.\cr - -Examples of oriloc outputs on real sequence data are there: -\url{https://pbil.univ-lyon1.fr/software/Oriloc/index.html}.\cr - The original paper for oriloc:\cr Frank, A.C., Lobry, J.R. (2000) Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. \emph{Bioinformatics},