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msbuild of the packages
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xieguigang committed Nov 12, 2024
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Expand Up @@ -24,7 +24,8 @@ <h3>Description</h3>

<p>Data model of a mgf ion

> <a href='http://www.matrixscience.com/help/data<em>file</em>help.html' title='http://www.matrixscience.com/help/data<em>file</em>help.html'>http://www.matrixscience.com/help/data<em>file</em>help.html</a></p>
> <a href='http://www.matrixscience.com/help/data_file_help.html' title='http://www.matrixscience.com/help/data_file_help.html'>http://www.matrixscience.com/help/data_file_help.html</a>
</p>

<h3>Declare</h3>

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Expand Up @@ -22,9 +22,9 @@ <h2>XcaliburRawFileIO</h2>

<h3>Description</h3>

<p>Class for reading Thermo Xcalibur <code>*.raw</code> files</p>
<p>Class for reading Thermo Xcalibur <code>*.raw</code> files

<p><a href='https://github.com/PNNL-Comp-Mass-Spec' title='https://github.com/PNNL-Comp-Mass-Spec'>https://github.com/PNNL-Comp-Mass-Spec</a></p>
<a href='https://github.com/PNNL-Comp-Mass-Spec' title='https://github.com/PNNL-Comp-Mass-Spec'>https://github.com/PNNL-Comp-Mass-Spec</a></p>

<h3>Declare</h3>

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Expand Up @@ -33,9 +33,7 @@ <h3>Description</h3>
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. <a href='https://doi.org/10.7554/eLife.70780' title='https://doi.org/10.7554/eLife.70780'>https://doi.org/10.7554/eLife.70780</a></p>

<p><a href='https://lotus.naturalproducts.net/' title='https://lotus.naturalproducts.net/'>https://lotus.naturalproducts.net/</a></p>
natural products research. eLife 11:e70780.;;;auto<em>url+1xxx;;;;;;auto</em>url+2xxx;;;</p>

<h3>Declare</h3>

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Expand Up @@ -28,10 +28,8 @@ <h4>Structure-data file</h4>
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 <a href='(http://www.lipidmaps.org/resources/downloads/index.html' title='(http://www.lipidmaps.org/resources/downloads/index.html'>(http://www.lipidmaps.org/resources/downloads/index.html</a>
+ PubChem FTP SDF<a href='(ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/SDF' title='(ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/SDF'>(ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/SDF</a></p>

<p><a href='https://cactus.nci.nih.gov/SDF<em>toolkit/' title='https://cactus.nci.nih.gov/SDF</em>toolkit/'>https://cactus.nci.nih.gov/SDF_toolkit/</a>
+ LMSD Structure-data file ;;;auto<em>url+1xxx;;; + PubChem FTP SDF;;;auto</em>url+2xxx;;;
<a href='https://cactus.nci.nih.gov/SDF_toolkit/' title='https://cactus.nci.nih.gov/SDF_toolkit/'>https://cactus.nci.nih.gov/SDF_toolkit/</a>

The SDF Toolkit in Perl 5

Expand All @@ -40,8 +38,7 @@ <h4>Structure-data file</h4>
Journal of Chemical Information and Computer Sciences
32:(3) 244-255, May-Jun 1992.

<a href='http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx' title='http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx'>http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx</a>
<a href='https://en.wikipedia.org/wiki/Chemical<em>table</em>file#SDF' title='https://en.wikipedia.org/wiki/Chemical<em>table</em>file#SDF'>https://en.wikipedia.org/wiki/Chemical<em>table</em>file#SDF</a></p>
;;;auto<em>url+4xxx;;;;;;auto</em>url+5xxx;;;</p>

<h3>Declare</h3>

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Expand Up @@ -22,9 +22,9 @@ <h2>Handle</h2>

<h3>Description</h3>

<p>进行网络之中的边连接的布局走向的<code>拐点</code>的矢量化描述</p>
<p>进行网络之中的边连接的布局走向的<code>拐点</code>的矢量化描述

<p><a href='https://github.com/cytoscape/cytoscape-impl/blob/93530ef3b35511d9b1fe0d0eb913ecdcd3b456a8/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/HandleImpl.java#L247' title='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</a></p>
<a href='https://github.com/cytoscape/cytoscape-impl/blob/93530ef3b35511d9b1fe0d0eb913ecdcd3b456a8/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/HandleImpl.java#L247' title='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</a></p>

<h3>Declare</h3>

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Expand Up @@ -47,7 +47,7 @@ <h3>Declare</h3>
Module: <a href="/vignettes/clr/Microsoft/VisualBasic/Text/Xml/Models/NamedValue.html">NamedValue[]</a>;
molWeight: double;
pathway: <a href="/vignettes/clr/Microsoft/VisualBasic/Text/Xml/Models/NamedValue.html">NamedValue[]</a>;
# The <a href="/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Compound.html">Compound</a>.<a href="#">entry</a>[compound] was involved in these reactions. <a href='(http://www.kegg.jp/dbget-bin/www<em>bget?rn:[' title='(http://www.kegg.jp/dbget-bin/www</em>bget?rn:['>(http://www.kegg.jp/dbget-bin/www<em>bget?rn:[</a>KEGG</em>Reaction_ID])
# The <a href="/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Compound.html">Compound</a>.<a href="#">entry</a>[compound] was involved in these reactions. <a href='(http://www.kegg.jp/dbget-bin/www_bget?rn:[KEGG_Reaction_ID])' title='(http://www.kegg.jp/dbget-bin/www_bget?rn:[KEGG_Reaction_ID])'>(http://www.kegg.jp/dbget-bin/www_bget?rn:[KEGG_Reaction_ID])</a>
reactionId: string;
remarks: string;
Stylesheet: <a href="/vignettes/clr/Microsoft/VisualBasic/ComponentModel/XmlStyleProcessor.html">XmlStyleProcessor</a>;
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3 changes: 3 additions & 0 deletions Rscript/Library/mzkit_app/vignettes/keywords.html
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Expand Up @@ -57,4 +57,7 @@ <h2>spatial</h2>
<h2>data visual</h2>
<p><a href="./mzplot/MsImaging/layer.html">MsImaging::layer</a>, <a href="./mzplot/MsImaging/defaultFilter.html">MsImaging::defaultFilter</a>, <a href="./mzplot/MsImaging/render.html">MsImaging::render</a></p>

<h2>ctype data</h2>
<p><a href="./mz_quantify/mzDeco/to_expression.html">mzDeco::to_expression</a>, <a href="./mz_quantify/mzDeco/to_matrix.html">mzDeco::to_matrix</a>, <a href="./mz_quantify/mzDeco/as.peak_set.html">mzDeco::as.peak_set</a></p>


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Expand Up @@ -49,7 +49,7 @@ <h3>Arguments</h3>

<h3 style="display: block;">Details</h3>

<p><a href='https://github.com/zhengfj1994/MRM-Ion<em>Pair</em>Finder' title='https://github.com/zhengfj1994/MRM-Ion<em>Pair</em>Finder'>https://github.com/zhengfj1994/MRM-Ion<em>Pair</em>Finder</a></p>
<p><a href='https://github.com/zhengfj1994/MRM-Ion_Pair_Finder' title='https://github.com/zhengfj1994/MRM-Ion_Pair_Finder'>https://github.com/zhengfj1994/MRM-Ion_Pair_Finder</a></p>

<h3 style="display: block">Authors</h3>

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Expand Up @@ -39,7 +39,7 @@ <h3>Arguments</h3>
<dd><p>the file path to the pubchem query search result file, the data file which
could be downloaded from the query result url example like:

> <a href='https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi?infmt=json&outfmt=xml&query={' title='https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi?infmt=json&outfmt=xml&query={'>https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi?infmt=json&outfmt=xml&query={</a>%22download%22:%22<em>%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</em>%22:%22kegg%22}]}}. [as string]</p></dd>
>;;;auto<em>url+1xxx;;;%22download%22:%22*%22,%22collection%22:%22compound%22,%22order%22:[%22relevancescore,desc%22],%22start%22:1,%22limit%22:10000000,%22downloadfilename%22:%22PubChem</em>compound<em>text</em>kegg%22,%22where%22:{%22ands%22:[{%22*%22:%22kegg%22}]}}. [as string]</p></dd>


<dt>convert.std</dt>
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2 changes: 1 addition & 1 deletion src/mzkit
Submodule mzkit updated from 570251 to 58a75b

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