diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MGF/Ions.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MGF/Ions.html
index 594620a621..c935f99f03 100644
--- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MGF/Ions.html
+++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MGF/Ions.html
@@ -24,7 +24,8 @@ Description
Data model of a mgf ion
- > http://www.matrixscience.com/help/datafilehelp.html
+ > http://www.matrixscience.com/help/data_file_help.html
+
Declare
diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ThermoRawFileReader/XcaliburRawFileIO.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ThermoRawFileReader/XcaliburRawFileIO.html
index 1a4bab4312..851a077d17 100644
--- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ThermoRawFileReader/XcaliburRawFileIO.html
+++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ThermoRawFileReader/XcaliburRawFileIO.html
@@ -22,9 +22,9 @@ XcaliburRawFileIO
Description
- Class for reading Thermo Xcalibur *.raw files
+ Class for reading Thermo Xcalibur *.raw files
-
https://github.com/PNNL-Comp-Mass-Spec
+https://github.com/PNNL-Comp-Mass-Spec
Declare
diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/Chemistry/LOTUS/NaturalProduct.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/Chemistry/LOTUS/NaturalProduct.html
index 7c2da9e93a..ba0fc5cb8d 100644
--- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/Chemistry/LOTUS/NaturalProduct.html
+++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/Chemistry/LOTUS/NaturalProduct.html
@@ -33,9 +33,7 @@ Description
Egon Willighagen, Arnaud Gaudry, James G Graham, Ralf Stephan, Roderic Page, Jiří
Vondrášek, Christoph Steinbeck, Guido F Pauli, Jean-Luc Wolfender, Jonathan Bisson,
Pierre-Marie Allard (2022) The LOTUS initiative for open knowledge management in
- natural products research. eLife 11:e70780. https://doi.org/10.7554/eLife.70780
-
-https://lotus.naturalproducts.net/
+ natural products research. eLife 11:e70780.;;;autourl+1xxx;;;;;;autourl+2xxx;;;
Declare
diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/SDF/SDF.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/SDF/SDF.html
index 28b6a04ecf..bb73d0f41f 100644
--- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/SDF/SDF.html
+++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/SDF/SDF.html
@@ -28,10 +28,8 @@ Structure-data file
to handle a list of molecular structures with associated properties.
The file format has been published (Dalby et al., J. Chem. Inf. Comput. Sci. 1992, 32: 244-255).
- + LMSD Structure-data file (http://www.lipidmaps.org/resources/downloads/index.html
- + PubChem FTP SDF(ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/SDF
-
-https://cactus.nci.nih.gov/SDF_toolkit/
+ + LMSD Structure-data file ;;;autourl+1xxx;;; + PubChem FTP SDF;;;autourl+2xxx;;;
+https://cactus.nci.nih.gov/SDF_toolkit/
The SDF Toolkit in Perl 5
@@ -40,8 +38,7 @@
Structure-data file
Journal of Chemical Information and Computer Sciences
32:(3) 244-255, May-Jun 1992.
- http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx
- https://en.wikipedia.org/wiki/Chemicaltablefile#SDF
+;;;autourl+4xxx;;;;;;autourl+5xxx;;;
Declare
diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Data/visualize/Network/Graph/EdgeBundling/Handle.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Data/visualize/Network/Graph/EdgeBundling/Handle.html
index 2df8908f03..6a6b376e2c 100644
--- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Data/visualize/Network/Graph/EdgeBundling/Handle.html
+++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Data/visualize/Network/Graph/EdgeBundling/Handle.html
@@ -22,9 +22,9 @@ Handle
Description
- 进行网络之中的边连接的布局走向的拐点的矢量化描述
+ 进行网络之中的边连接的布局走向的拐点的矢量化描述
-
https://github.com/cytoscape/cytoscape-impl/blob/93530ef3b35511d9b1fe0d0eb913ecdcd3b456a8/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/HandleImpl.java#L247
+https://github.com/cytoscape/cytoscape-impl/blob/93530ef3b35511d9b1fe0d0eb913ecdcd3b456a8/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/HandleImpl.java#L247
Declare
diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Compound.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Compound.html
index 7dd6d8d590..6ce3a9eea6 100644
--- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Compound.html
+++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Compound.html
@@ -47,7 +47,7 @@ Declare
Module: NamedValue[];
molWeight: double;
pathway: NamedValue[];
- # The Compound.entry[compound] was involved in these reactions. (http://www.kegg.jp/dbget-bin/wwwbget?rn:[KEGGReaction_ID])
+ # The Compound.entry[compound] was involved in these reactions. (http://www.kegg.jp/dbget-bin/www_bget?rn:[KEGG_Reaction_ID])
reactionId: string;
remarks: string;
Stylesheet: XmlStyleProcessor;
diff --git a/Rscript/Library/mzkit_app/vignettes/keywords.html b/Rscript/Library/mzkit_app/vignettes/keywords.html
index c532349e9e..bc98174e7a 100644
--- a/Rscript/Library/mzkit_app/vignettes/keywords.html
+++ b/Rscript/Library/mzkit_app/vignettes/keywords.html
@@ -57,4 +57,7 @@ spatial
data visual
MsImaging::layer, MsImaging::defaultFilter, MsImaging::render
+ctype data
+mzDeco::to_expression, mzDeco::to_matrix, mzDeco::as.peak_set
+
diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/find_untargeted_ionpair.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/find_untargeted_ionpair.html
index 3a15f5ecaa..47f7cbff6f 100644
--- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/find_untargeted_ionpair.html
+++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/find_untargeted_ionpair.html
@@ -49,7 +49,7 @@ Arguments
Details
- https://github.com/zhengfj1994/MRM-IonPairFinder
+ https://github.com/zhengfj1994/MRM-Ion_Pair_Finder
Authors
diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.webquery.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.webquery.html
index 99f842f4d6..2ddbec4c24 100644
--- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.webquery.html
+++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.webquery.html
@@ -39,7 +39,7 @@ Arguments
the file path to the pubchem query search result file, the data file which
could be downloaded from the query result url example like:
- > https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi?infmt=json&outfmt=xml&query={%22download%22:%22%22,%22collection%22:%22compound%22,%22order%22:[%22relevancescore,desc%22],%22start%22:1,%22limit%22:10000000,%22downloadfilename%22:%22PubChem_compound_text_kegg%22,%22where%22:{%22ands%22:[{%22%22:%22kegg%22}]}}. [as string]
+ >;;;autourl+1xxx;;;%22download%22:%22*%22,%22collection%22:%22compound%22,%22order%22:[%22relevancescore,desc%22],%22start%22:1,%22limit%22:10000000,%22downloadfilename%22:%22PubChemcompoundtextkegg%22,%22where%22:{%22ands%22:[{%22*%22:%22kegg%22}]}}. [as string]
convert.std
diff --git a/src/mzkit b/src/mzkit
index 5702514ae1..58a75b8421 160000
--- a/src/mzkit
+++ b/src/mzkit
@@ -1 +1 @@
-Subproject commit 5702514ae10763d21a8ec6b2d7b8cef2baae502d
+Subproject commit 58a75b84210b7c5206ac466995daff5856bd10e7