Renamed msd_mutate to mutate_msd

.Rbuildignore

@@ -3,4 +3,5 @@
 ^\.travis\.yml$
 ^binder/*$
 ^notebooks/*$
-^LICENSE$
+^LICENSE$
+^docs/*$

DESCRIPTION

@@ -2,8 +2,8 @@ Package: GoldenMutagenesis
 Type: Package
 Encoding: UTF-8
 Title: A tool to calculate and validate primers for Golden Gate Cloning
-Version: 1.1.0
-Date: 2019-01-21
+Version: 1.1.1
+Date: 2019-05-13
 Author: Chris Ulpinnis & Pascal Püllmann
 Maintainer: Chris Ulpinnis <Chris.Ulpinnis@ipb-halle.de>
 Description: The Golden Gate cloning technique has been proven to be a highly efficient toolbox for a variety of cloning setups. Based on its modular concept it is particularly suitable for the use in multiple-site mutagenesis approaches. In this technical note we developed a protocol termed Golden Mutagenesis for the rapid, easy, reliable and cheap formation of mutagenesis libraries. One to five positions could be altered in parallel or simultaneously within two days. To facilitate the implementation of this technique, this R-library has been developed for the automated primer design and the graphical evaluation of sequencing results to determine the quality of the library.

GoldenMutagenesis.Rproj

@@ -15,4 +15,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace,vignette
+PackageRoxygenize: rd,collate,namespace

NAMESPACE

@@ -4,7 +4,7 @@ export(base_distribution)
 export(domesticate)
 export(get_cu_table)
 export(list_cu_table)
-export(msd_mutate)
+export(mutate_msd)
 export(mutate_spm)
 export(primer_add_level)
 export(primer_prepare_level)

R/exported_functions.R

@@ -515,12 +515,12 @@ mutate_spm<-function(input_sequence, prefix="TT" ,restriction_enzyme="GGTCTC", s
 #' data(MSD_BsaI_setup_lv2)
 #' print(mutations)
 #' print(recognition_site_bsai)
-#' primers<-msd_mutate(input_sequence, prefix="TT" ,
+#' primers<-mutate_msd(input_sequence, prefix="TT" ,
 #' restriction_enzyme=recognition_site_bsai, suffix="A", 
 #' vector=c("AATG", "AAGC"), replacements=mutations, replacement_range=5,
 #' binding_min_length=4 , binding_max_length=9, target_temp=60,
 #' fragment_min_size=60 )
-msd_mutate<-function(input_sequence, codon="NDT" ,prefix="TT" ,restriction_enzyme="GGTCTC", suffix="A", vector=c("AATG", "AAGC"), replacements, replacement_range=5, binding_min_length=4 ,binding_max_length=9, target_temp=60, fragment_min_size=100 ) {
+mutate_msd<-function(input_sequence, codon="NDT" ,prefix="TT" ,restriction_enzyme="GGTCTC", suffix="A", vector=c("AATG", "AAGC"), replacements, replacement_range=5, binding_min_length=4 ,binding_max_length=9, target_temp=60, fragment_min_size=100 ) {
   codon<-str_to_upper(codon)
   prefix<-str_to_upper(prefix)
   suffix<-str_to_upper(suffix)

README.md

@@ -49,8 +49,12 @@ Control](https://ipb-halle.github.io/GoldenMutagenesis/articles/QQC.html)
 ## Interactive Example
 
 ## Webtool Beta Version
-**You can try our webtool at http://msbi.ipb-halle.de/GoldenMutagenesisWeb or on binderhub at [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/ipb-halle/GoldenMutagenesisWeb/master?urlpath=shiny).** \
-The Webtools git repository is available at: https://github.com/ipb-halle/GoldenMutagenesisWeb \
+**You can try our webtool at http://msbi.ipb-halle.de/GoldenMutagenesisWeb or on binderhub at [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/ipb-halle/GoldenMutagenesisWeb/master?urlpath=shiny).** 
+
+
+The Webtools git repository is available at: https://github.com/ipb-halle/GoldenMutagenesisWeb 
+
+
 *Please note that the webtool is still in beta phase. There are still errors and also the user interface is not the final user experience. If you encounter any problems please send an email to me.*