[Seqinr-commits] r2106 - in pkg: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Oct 9 15:13:13 CEST 2020
Author: simonpenel
Date: 2020-10-09 15:13:13 +0200 (Fri, 09 Oct 2020)
New Revision: 2106
Modified:
pkg/DESCRIPTION
pkg/man/SEQINR.UTIL.Rd
pkg/man/a.Rd
pkg/man/aaa.Rd
pkg/man/amb.Rd
pkg/man/bma.Rd
pkg/man/computePI.Rd
pkg/man/dinucl.Rd
pkg/man/get.db.growth.Rd
pkg/man/oriloc.Rd
pkg/man/prochlo.Rd
pkg/man/recstat.Rd
pkg/man/translate.Rd
pkg/man/uco.Rd
pkg/man/zscore.Rd
Log:
Updated urls
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/DESCRIPTION 2020-10-09 13:13:13 UTC (rev 2106)
@@ -1,7 +1,7 @@
Encoding: UTF-8
Package: seqinr
-Version: 4.2-3
-Date: 2020-10-1
+Version: 4.2-4
+Date: 2020-10-8
Title: Biological Sequences Retrieval and Analysis
Authors at R: c(person("Delphine", "Charif", role = "aut"),
person("Olivier", "Clerc", role = "ctb"),
Modified: pkg/man/SEQINR.UTIL.Rd
===================================================================
--- pkg/man/SEQINR.UTIL.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/SEQINR.UTIL.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -15,7 +15,7 @@
}
}
\source{
-Data prepared by D. Charif.\cr The genetic codes have been taken from the ncbi database: \url{https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi}. Last visited on 2016-10-05 corresponding to last update of the Genetic Codes: April 30, 2013.\cr The IUPAC one-letter code for aminoacids is descibed at: \url{http://www.chem.qmul.ac.uk/iupac/AminoAcid/}.
+Data prepared by D. Charif.\cr The genetic codes have been taken from the ncbi database: \url{https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi}. Last visited on 2016-10-05 corresponding to last update of the Genetic Codes: April 30, 2013.\cr The IUPAC one-letter code for aminoacids is descibed at: \url{https://www.bioinformatics.org/sms/iupac.html}.
pK values of amino acids were taken from Bjellqvist et al.\cr
Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez, J.-Ch., Frutiger, S. & Hochstrasser, D.F.(1993) The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences.\emph{ Electrophoresis}, \bold{14}, 1023-1031.
}
Modified: pkg/man/a.Rd
===================================================================
--- pkg/man/a.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/a.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -22,7 +22,7 @@
}
\references{
The IUPAC one-letter code for aminoacids is described at:
-\url{http://www.chem.qmul.ac.uk/iupac/AminoAcid/}\cr
+\url{https://www.bioinformatics.org/sms/iupac.html}\cr
\code{citation("seqinr")}
}
\author{D. Charif, J.R. Lobry }
Modified: pkg/man/aaa.Rd
===================================================================
--- pkg/man/aaa.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/aaa.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -20,7 +20,7 @@
}
\references{
The IUPAC one-letter code for aminoacids is described at:
-\url{http://www.chem.qmul.ac.uk/iupac/AminoAcid/}
+\url{https://www.bioinformatics.org/sms/iupac.html}
\code{citation("seqinr")}
}
\author{J.R. Lobry}
Modified: pkg/man/amb.Rd
===================================================================
--- pkg/man/amb.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/amb.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -26,7 +26,7 @@
\references{
The nomenclature for incompletely specified bases in nucleic acid sequences
-at: \url{http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html}
+at: \url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC341218/}
\code{citation("seqinr")}
}
Modified: pkg/man/bma.Rd
===================================================================
--- pkg/man/bma.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/bma.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -23,7 +23,7 @@
\references{
The nomenclature for incompletely specified bases in nucleic acid sequences
-at: \url{http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html}
+at: \url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC341218/}
\code{citation("seqinr")}
}
Modified: pkg/man/computePI.Rd
===================================================================
--- pkg/man/computePI.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/computePI.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -16,7 +16,7 @@
}
\references{
The algorithm is the same as the one which is implemented at the following url:
-\url{http://www.expasy.org/tools/pi_tool-doc.html} but with many trials
+\url{https://web.expasy.org/compute_pi/pi_tool-doc.html} but with many trials
in case of convergence failure of the non-linear regression procedure.
\code{citation("seqinr")}
}
Modified: pkg/man/dinucl.Rd
===================================================================
--- pkg/man/dinucl.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/dinucl.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -27,7 +27,7 @@
are not depleted in light-exposed Prokaryotic genomes.
\emph{Molecular Biology and Evolution},
\bold{23}:2214-2219.\cr
- \url{http://mbe.oxfordjournals.org/cgi/reprint/23/11/2214}\cr\cr
+ \url{https://academic.oup.com/mbe/article/23/11/2214/1335460}\cr\cr
\code{citation("seqinr")}
}
Modified: pkg/man/get.db.growth.Rd
===================================================================
--- pkg/man/get.db.growth.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/get.db.growth.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -33,7 +33,7 @@
At that time the doubling time was 16.9 months. This is an
update in 2016 from release 3.1-5 of the seqinr tutorial
-\url{http://seqinr.r-forge.r-project.org/seqinr_3_1-5.pdf}:
+\url{https://seqinr.r-forge.r-project.org/seqinr_3_1-5.pdf}:
\if{html}{\figure{introduction-dbg.pdf}{options: width=400}}
\if{latex}{\figure{introduction-dbg.pdf}{options: width=12cm}}
Modified: pkg/man/oriloc.Rd
===================================================================
--- pkg/man/oriloc.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/oriloc.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -81,7 +81,7 @@
A simple informal introduction to DNA-walks:\cr
Lobry, J.R. (1999) Genomic landscapes. \emph{Microbiology Today},
\bold{26}:164-165.\cr
-\url{http://seqinr.r-forge.r-project.org/MicrTod_1999_26_164.pdf}\cr\cr
+\url{https://seqinr.r-forge.r-project.org/MicrTod_1999_26_164.pdf}\cr\cr
An early and somewhat historical application of DNA-walks:\cr
Lobry, J.R. (1996) A simple vectorial representation of DNA sequences
@@ -89,7 +89,7 @@
\bold{78}:323-326.\cr
Glimmer, a very efficient open source software for the prediction of CDS from scratch
-in prokaryotic genome, is decribed at \url{http://www.cbcb.umd.edu/software/glimmer/}.\cr
+in prokaryotic genome, is decribed at \url{http://ccb.jhu.edu/software/glimmer/index.shtml}.\cr
For a description of Glimmer 1.0 and 2.0 see:\cr
Delcher, A.L., Harmon, D., Kasif, S., White, O., Salzberg, S.L. (1999)
Modified: pkg/man/prochlo.Rd
===================================================================
--- pkg/man/prochlo.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/prochlo.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -30,7 +30,7 @@
are not depleted in light-exposed Prokaryotic genomes.
\emph{Molecular Biology and Evolution},
\bold{23}:2214-2219.\cr
- \url{http://mbe.oxfordjournals.org/cgi/reprint/23/11/2214}\cr\cr
+ \url{https://academic.oup.com/mbe/article/23/11/2214/1335460}\cr\cr
\code{citation("seqinr")}
}
Modified: pkg/man/recstat.Rd
===================================================================
--- pkg/man/recstat.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/recstat.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -50,7 +50,7 @@
Fichant, G., Gautier, C. (1987) Statistical method for predicting protein coding
regions in nucleic acid sequences. \emph{Comput. Appl. Biosci.}, \bold{3}, 287--295.\cr
-\url{http://bioinformatics.oxfordjournals.org/content/3/4/287.abstract}\cr
+\url{https://academic.oup.com/bioinformatics/article-abstract/3/4/287/218186}\cr
}
\seealso{\code{\link{draw.recstat}}, \code{\link{test.li.recstat}}, \code{\link{test.co.recstat}}}
\examples{
Modified: pkg/man/translate.Rd
===================================================================
--- pkg/man/translate.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/translate.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -57,7 +57,7 @@
\url{https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi}.
Last update October 05, 2000.\cr
The IUPAC one-letter code for aminoacids is described at:
-\url{http://www.chem.qmul.ac.uk/iupac/AminoAcid/}
+\url{https://www.bioinformatics.org/sms/iupac.html}
\code{citation("seqinr")}
}
Modified: pkg/man/uco.Rd
===================================================================
--- pkg/man/uco.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/uco.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -83,7 +83,7 @@
Suzuki, H., Brown, C.J., Forney, L.J., Top, E. (2008)
Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria.
-\emph{DNA Research}, \bold{15}:357-365. \url{http://dnaresearch.oxfordjournals.org/cgi/reprint/15/6/357}.
+\emph{DNA Research}, \bold{15}:357-365. \url{https://academic.oup.com/dnaresearch/article/15/6/357/513030}.
}
\author{D. Charif, J.R. Lobry, G. Perrière}
Modified: pkg/man/zscore.Rd
===================================================================
--- pkg/man/zscore.Rd 2020-10-01 09:15:39 UTC (rev 2105)
+++ pkg/man/zscore.Rd 2020-10-09 13:13:13 UTC (rev 2106)
@@ -88,7 +88,7 @@
are not depleted in light-exposed Prokaryotic genomes.
\emph{Molecular Biology and Evolution},
\bold{23}:2214-2219.
- \url{http://mbe.oxfordjournals.org/cgi/reprint/23/11/2214}
+ \url{https://academic.oup.com/mbe/article/23/11/2214/1335460}
\code{citation("seqinr")}
}
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