From 17b29251f583aa0f43fd11d4e8497ca90a560e78 Mon Sep 17 00:00:00 2001
From: tonywu1999 <anthonywu92@gmail.com>
Date: Tue, 27 Aug 2024 18:14:16 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20Vitek-La?=
 =?UTF-8?q?b/MSstatsBioNet@f8aa0f8cfdd81d813483ec2b80faa6334ddf9a83=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                              | 2 +-
 LICENSE-text.html                     | 2 +-
 articles/MSstatsBioNet.html           | 4 ++--
 articles/index.html                   | 2 +-
 authors.html                          | 6 +++---
 index.html                            | 2 +-
 news/index.html                       | 2 +-
 pkgdown.yml                           | 2 +-
 reference/getSubnetworkFromIndra.html | 2 +-
 reference/index.html                  | 2 +-
 reference/visualizeNetworks.html      | 2 +-
 search.json                           | 2 +-
 12 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/404.html b/404.html
index 77a0692..0c85ee7 100644
--- a/404.html
+++ b/404.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="https://vitek-lab.github.io/MSstatsBioNet/index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index ebe6236..9e261b2 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/MSstatsBioNet.html b/articles/MSstatsBioNet.html
index b0cfa73..d9f756e 100644
--- a/articles/MSstatsBioNet.html
+++ b/articles/MSstatsBioNet.html
@@ -20,7 +20,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -118,7 +118,7 @@ <h2 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#s
 <span><span class="co">#&gt; [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; other attached packages:</span></span>
-<span><span class="co">#&gt; [1] MSstatsBioNet_0.99.0</span></span>
+<span><span class="co">#&gt; [1] MSstatsBioNet_0.99.1</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; loaded via a namespace (and not attached):</span></span>
 <span><span class="co">#&gt;  [1] base64url_1.4       jsonlite_1.8.8      compiler_4.4.1     </span></span>
diff --git a/articles/index.html b/articles/index.html
index 7d93e41..a32d658 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index f48ccd3..7e3b663 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -50,13 +50,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Wu A, Vitek O (2024).
 <em>MSstatsBioNet: Network Analysis for MS-based Proteomics Experiments</em>.
-R package version 0.99.0, https://vitek-lab.github.io/MSstatsBioNet/, <a href="http://msstats.org" class="external-link">http://msstats.org</a>.
+R package version 0.99.1, https://vitek-lab.github.io/MSstatsBioNet/, <a href="http://msstats.org" class="external-link">http://msstats.org</a>.
 </p>
       <pre>@Manual{,
   title = {MSstatsBioNet: Network Analysis for MS-based Proteomics Experiments},
   author = {Anthony Wu and Olga Vitek},
   year = {2024},
-  note = {R package version 0.99.0, https://vitek-lab.github.io/MSstatsBioNet/},
+  note = {R package version 0.99.1, https://vitek-lab.github.io/MSstatsBioNet/},
   url = {http://msstats.org},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index c9771c2..bfd6bdc 100644
--- a/index.html
+++ b/index.html
@@ -22,7 +22,7 @@
 
     <a class="navbar-brand me-2" href="index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/news/index.html b/news/index.html
index dac1046..ea5191d 100644
--- a/news/index.html
+++ b/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/pkgdown.yml b/pkgdown.yml
index 31f4c8f..fa860cc 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.0
 pkgdown_sha: ~
 articles:
   MSstatsBioNet: MSstatsBioNet.html
-last_built: 2024-08-27T18:12Z
+last_built: 2024-08-27T18:14Z
 urls:
   reference: https://vitek-lab.github.io/MSstatsBioNet/reference
   article: https://vitek-lab.github.io/MSstatsBioNet/articles
diff --git a/reference/getSubnetworkFromIndra.html b/reference/getSubnetworkFromIndra.html
index 610582c..21ef5b9 100644
--- a/reference/getSubnetworkFromIndra.html
+++ b/reference/getSubnetworkFromIndra.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index d00b93b..eb5180b 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/visualizeNetworks.html b/reference/visualizeNetworks.html
index e07f8c4..0a901fe 100644
--- a/reference/visualizeNetworks.html
+++ b/reference/visualizeNetworks.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">MSstatsBioNet</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index 4feb507..a27996c 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"purpose-of-msstatsbionet","dir":"Articles","previous_headings":"","what":"Purpose of MSstatsBioNet","title":"MSstatsBioNet","text":"MSstatsBioNet package member MSstats family packages. contains set functions interpretation mass spectrometry (MS) statistical analysis results context protein-protein interaction networks. package designed used conjunction MSstats package. package provides function getSubnetworkFromIndra retrieves subnetwork proteins INDRA database based differential abundance analysis results. function visualizeNetworks takes output getSubnetworkFromIndra visualizes subnetwork. package distributed Artistic-2.0 license. However, dependencies may different licenses. example, getSubnetworkFromIndra depends INDRA, distributed BSD 2-Clause license. Furthermore, INDRA’s knowledge sources may different licenses commercial applications. Please refer INDRA README information knowledge sources associated licenses.","code":"input <- data.table::fread(     system.file(\"processed_data/groupComparisonModel.csv\",         package = \"MSstatsBioNet\"     ) ) subnetwork <- getSubnetworkFromIndra(input) visualizeNetworks(subnetwork$nodes, subnetwork$edges)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"MSstatsBioNet","text":"","code":"sessionInfo() #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.4 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] MSstatsBioNet_0.99.0 #>  #> loaded via a namespace (and not attached): #>  [1] base64url_1.4       jsonlite_1.8.8      compiler_4.4.1      #>  [4] crayon_1.5.3        gtools_3.9.5        IRdisplay_1.1       #>  [7] bitops_1.0-8        RCy3_2.24.0         jquerylib_0.1.4     #> [10] systemfonts_1.1.0   textshaping_0.4.0   uuid_1.2-1          #> [13] yaml_2.3.10         fastmap_1.2.0       IRkernel_1.3.2      #> [16] R6_2.5.1            knitr_1.48          backports_1.5.0     #> [19] BiocGenerics_0.50.0 graph_1.82.0        XML_3.99-0.17       #> [22] desc_1.4.3          bslib_0.8.0         pillar_1.9.0        #> [25] RColorBrewer_1.1-3  rlang_1.1.4         utf8_1.2.4          #> [28] cachem_1.1.0        stringi_1.8.4       repr_1.1.7          #> [31] xfun_0.47           caTools_1.18.2      fs_1.6.4            #> [34] sass_0.4.9          RJSONIO_1.3-1.9     cli_3.6.3           #> [37] pkgdown_2.1.0       digest_0.6.37       base64enc_0.1-3     #> [40] pbdZMQ_0.3-11       lifecycle_1.0.4     r2r_0.1.1           #> [43] vctrs_0.6.5         KernSmooth_2.23-24  evaluate_0.24.0     #> [46] glue_1.7.0          ragg_1.3.2          stats4_4.4.1        #> [49] RCurl_1.98-1.16     fansi_1.0.6         rmarkdown_2.28      #> [52] httr_1.4.7          gplots_3.1.3.1      tools_4.4.1         #> [55] htmltools_0.5.8.1"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Anthony Wu. Author, maintainer. Olga Vitek. Author.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Wu , Vitek O (2024). MSstatsBioNet: Network Analysis MS-based Proteomics Experiments. R package version 0.99.0, https://vitek-lab.github.io/MSstatsBioNet/, http://msstats.org.","code":"@Manual{,   title = {MSstatsBioNet: Network Analysis for MS-based Proteomics Experiments},   author = {Anthony Wu and Olga Vitek},   year = {2024},   note = {R package version 0.99.0, https://vitek-lab.github.io/MSstatsBioNet/},   url = {http://msstats.org}, }"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"msstatsbionet","dir":"","previous_headings":"","what":"Network Analysis for MS-based Proteomics Experiments","title":"Network Analysis for MS-based Proteomics Experiments","text":"package provides suite functions query various network databases, filter queries & results, visualize networks.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"installation-instructions","dir":"","previous_headings":"","what":"Installation Instructions","title":"Network Analysis for MS-based Proteomics Experiments","text":"install package bioconductor, run following command: can install development version package Github:","code":"if (!require(\"BiocManager\", quietly = TRUE))     install.packages(\"BiocManager\")  BiocManager::install(\"MSstatsBioNet\") devtools::install_github(\"Vitek-Lab/MSstatsConvert\", build_vignettes = TRUE)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Network Analysis for MS-based Proteomics Experiments","text":"package distributed Artistic-2.0 license. However, dependencies may different licenses. Notably, INDRA distributed BSD 2-Clause license. Furthermore, INDRA’s knowledge sources may different licenses commercial applications. Please refer INDRA README information knowledge sources associated licenses.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"databases-supported","dir":"","previous_headings":"","what":"Databases Supported","title":"Network Analysis for MS-based Proteomics Experiments","text":"INDRA","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"filtering-options-supported","dir":"","previous_headings":"","what":"Filtering Options Supported","title":"Network Analysis for MS-based Proteomics Experiments","text":"P-Value Filter","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"visualization-options-supported","dir":"","previous_headings":"","what":"Visualization Options Supported","title":"Network Analysis for MS-based Proteomics Experiments","text":"Cytoscape Desktop","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":null,"dir":"Reference","previous_headings":"","what":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"Get subnetwork INDRA database differential analysis results","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"","code":"getSubnetworkFromIndra(input, pvalue_cutoff = NULL)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"input groupComparison comparisionResult table additional HGNC ID HGNC name columns pvalue_cutoff p-value cutoff filtering. Default NULL, .e. filtering","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"list 2 data.frames, nodes edges","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"","code":"input <- data.table::fread(system.file(     \"processed_data/groupComparisonModel.csv\",     package = \"MSstatsBioNet\" )) # subnetwork = getSubnetworkFromIndra(input, pvalue_cutoff = 0.05) # head(subnetwork$nodes) # head(subnetwork$edges)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":null,"dir":"Reference","previous_headings":"","what":"Create visualization of subnetwork in cytoscape — visualizeNetworks","title":"Create visualization of subnetwork in cytoscape — visualizeNetworks","text":"Create visualization subnetwork cytoscape","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create visualization of subnetwork in cytoscape — visualizeNetworks","text":"","code":"visualizeNetworks(nodes, edges, pvalue_cutoff = 0.05, logfc_cutoff = 0.5)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create visualization of subnetwork in cytoscape — visualizeNetworks","text":"nodes dataframe nodes edges dataframe edges pvalue_cutoff p-value cutoff coloring significant proteins. Default 0.05 logfc_cutoff log fold change cutoff coloring significant proteins. Default 0.5","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create visualization of subnetwork in cytoscape — visualizeNetworks","text":"cytoscape visualization subnetwork","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create visualization of subnetwork in cytoscape — visualizeNetworks","text":"","code":"input <- data.table::fread(system.file(     \"processed_data/groupComparisonModel.csv\",     package = \"MSstatsBioNet\" )) # subnetwork = getSubnetworkFromIndra(input) # visualizeNetworks(subnetwork$nodes, subnetwork$edges)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/news/index.html","id":"msstatsbionet-0990","dir":"Changelog","previous_headings":"","what":"MSstatsBioNet 0.99.0","title":"MSstatsBioNet 0.99.0","text":"Added function getSubnetworkFromIndra extract biomolecular subnetworks INDRA database. Added function visualizeNetworks visualize networks Cytoscape desktop. Added vignette","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/news/index.html","id":"msstatsbionet-010","dir":"Changelog","previous_headings":"","what":"MSstatsBioNet 0.1.0","title":"MSstatsBioNet 0.1.0","text":"Added NEWS.md file track changes package.","code":""}]
+[{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"purpose-of-msstatsbionet","dir":"Articles","previous_headings":"","what":"Purpose of MSstatsBioNet","title":"MSstatsBioNet","text":"MSstatsBioNet package member MSstats family packages. contains set functions interpretation mass spectrometry (MS) statistical analysis results context protein-protein interaction networks. package designed used conjunction MSstats package. package provides function getSubnetworkFromIndra retrieves subnetwork proteins INDRA database based differential abundance analysis results. function visualizeNetworks takes output getSubnetworkFromIndra visualizes subnetwork. package distributed Artistic-2.0 license. However, dependencies may different licenses. example, getSubnetworkFromIndra depends INDRA, distributed BSD 2-Clause license. Furthermore, INDRA’s knowledge sources may different licenses commercial applications. Please refer INDRA README information knowledge sources associated licenses.","code":"input <- data.table::fread(     system.file(\"processed_data/groupComparisonModel.csv\",         package = \"MSstatsBioNet\"     ) ) subnetwork <- getSubnetworkFromIndra(input) visualizeNetworks(subnetwork$nodes, subnetwork$edges)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/articles/MSstatsBioNet.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"MSstatsBioNet","text":"","code":"sessionInfo() #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.4 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] MSstatsBioNet_0.99.1 #>  #> loaded via a namespace (and not attached): #>  [1] base64url_1.4       jsonlite_1.8.8      compiler_4.4.1      #>  [4] crayon_1.5.3        gtools_3.9.5        IRdisplay_1.1       #>  [7] bitops_1.0-8        RCy3_2.24.0         jquerylib_0.1.4     #> [10] systemfonts_1.1.0   textshaping_0.4.0   uuid_1.2-1          #> [13] yaml_2.3.10         fastmap_1.2.0       IRkernel_1.3.2      #> [16] R6_2.5.1            knitr_1.48          backports_1.5.0     #> [19] BiocGenerics_0.50.0 graph_1.82.0        XML_3.99-0.17       #> [22] desc_1.4.3          bslib_0.8.0         pillar_1.9.0        #> [25] RColorBrewer_1.1-3  rlang_1.1.4         utf8_1.2.4          #> [28] cachem_1.1.0        stringi_1.8.4       repr_1.1.7          #> [31] xfun_0.47           caTools_1.18.2      fs_1.6.4            #> [34] sass_0.4.9          RJSONIO_1.3-1.9     cli_3.6.3           #> [37] pkgdown_2.1.0       digest_0.6.37       base64enc_0.1-3     #> [40] pbdZMQ_0.3-11       lifecycle_1.0.4     r2r_0.1.1           #> [43] vctrs_0.6.5         KernSmooth_2.23-24  evaluate_0.24.0     #> [46] glue_1.7.0          ragg_1.3.2          stats4_4.4.1        #> [49] RCurl_1.98-1.16     fansi_1.0.6         rmarkdown_2.28      #> [52] httr_1.4.7          gplots_3.1.3.1      tools_4.4.1         #> [55] htmltools_0.5.8.1"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Anthony Wu. Author, maintainer. Olga Vitek. Author.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Wu , Vitek O (2024). MSstatsBioNet: Network Analysis MS-based Proteomics Experiments. R package version 0.99.1, https://vitek-lab.github.io/MSstatsBioNet/, http://msstats.org.","code":"@Manual{,   title = {MSstatsBioNet: Network Analysis for MS-based Proteomics Experiments},   author = {Anthony Wu and Olga Vitek},   year = {2024},   note = {R package version 0.99.1, https://vitek-lab.github.io/MSstatsBioNet/},   url = {http://msstats.org}, }"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"msstatsbionet","dir":"","previous_headings":"","what":"Network Analysis for MS-based Proteomics Experiments","title":"Network Analysis for MS-based Proteomics Experiments","text":"package provides suite functions query various network databases, filter queries & results, visualize networks.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"installation-instructions","dir":"","previous_headings":"","what":"Installation Instructions","title":"Network Analysis for MS-based Proteomics Experiments","text":"install package bioconductor, run following command: can install development version package Github:","code":"if (!require(\"BiocManager\", quietly = TRUE))     install.packages(\"BiocManager\")  BiocManager::install(\"MSstatsBioNet\") devtools::install_github(\"Vitek-Lab/MSstatsConvert\", build_vignettes = TRUE)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Network Analysis for MS-based Proteomics Experiments","text":"package distributed Artistic-2.0 license. However, dependencies may different licenses. Notably, INDRA distributed BSD 2-Clause license. Furthermore, INDRA’s knowledge sources may different licenses commercial applications. Please refer INDRA README information knowledge sources associated licenses.","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"databases-supported","dir":"","previous_headings":"","what":"Databases Supported","title":"Network Analysis for MS-based Proteomics Experiments","text":"INDRA","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"filtering-options-supported","dir":"","previous_headings":"","what":"Filtering Options Supported","title":"Network Analysis for MS-based Proteomics Experiments","text":"P-Value Filter","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/index.html","id":"visualization-options-supported","dir":"","previous_headings":"","what":"Visualization Options Supported","title":"Network Analysis for MS-based Proteomics Experiments","text":"Cytoscape Desktop","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":null,"dir":"Reference","previous_headings":"","what":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"Get subnetwork INDRA database differential analysis results","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"","code":"getSubnetworkFromIndra(input, pvalue_cutoff = NULL)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"input groupComparison comparisionResult table additional HGNC ID HGNC name columns pvalue_cutoff p-value cutoff filtering. Default NULL, .e. filtering","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"list 2 data.frames, nodes edges","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/getSubnetworkFromIndra.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get subnetwork from INDRA database with differential analysis results — getSubnetworkFromIndra","text":"","code":"input <- data.table::fread(system.file(     \"processed_data/groupComparisonModel.csv\",     package = \"MSstatsBioNet\" )) # subnetwork = getSubnetworkFromIndra(input, pvalue_cutoff = 0.05) # head(subnetwork$nodes) # head(subnetwork$edges)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":null,"dir":"Reference","previous_headings":"","what":"Create visualization of subnetwork in cytoscape — visualizeNetworks","title":"Create visualization of subnetwork in cytoscape — visualizeNetworks","text":"Create visualization subnetwork cytoscape","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create visualization of subnetwork in cytoscape — visualizeNetworks","text":"","code":"visualizeNetworks(nodes, edges, pvalue_cutoff = 0.05, logfc_cutoff = 0.5)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create visualization of subnetwork in cytoscape — visualizeNetworks","text":"nodes dataframe nodes edges dataframe edges pvalue_cutoff p-value cutoff coloring significant proteins. Default 0.05 logfc_cutoff log fold change cutoff coloring significant proteins. Default 0.5","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create visualization of subnetwork in cytoscape — visualizeNetworks","text":"cytoscape visualization subnetwork","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/reference/visualizeNetworks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create visualization of subnetwork in cytoscape — visualizeNetworks","text":"","code":"input <- data.table::fread(system.file(     \"processed_data/groupComparisonModel.csv\",     package = \"MSstatsBioNet\" )) # subnetwork = getSubnetworkFromIndra(input) # visualizeNetworks(subnetwork$nodes, subnetwork$edges)"},{"path":"https://vitek-lab.github.io/MSstatsBioNet/news/index.html","id":"msstatsbionet-0990","dir":"Changelog","previous_headings":"","what":"MSstatsBioNet 0.99.0","title":"MSstatsBioNet 0.99.0","text":"Added function getSubnetworkFromIndra extract biomolecular subnetworks INDRA database. Added function visualizeNetworks visualize networks Cytoscape desktop. Added vignette","code":""},{"path":"https://vitek-lab.github.io/MSstatsBioNet/news/index.html","id":"msstatsbionet-010","dir":"Changelog","previous_headings":"","what":"MSstatsBioNet 0.1.0","title":"MSstatsBioNet 0.1.0","text":"Added NEWS.md file track changes package.","code":""}]