Bioconductor Code: Browse

Browse code

test

guangchuang yu authored on 03/01/2017 10:11:07
Showing 14 changed files

.gitmodules index 00000000..e69de29b
docs/featuredArticles/index.html index dddae1ac..31813a26 100644
docs/mkdocs/search_index.json index d556299f..ad37a815 100644
mkdocs/docs/featuredArticles.md index d269ddf4..ba59c88a 100644
mkdocs/mysoftware index bfcc3e40..00000000
mkdocs/mysoftware/ChIPseeker.md index 00000000..90b8002f
mkdocs/mysoftware/DOSE.md index 00000000..aee9b48a
mkdocs/mysoftware/GOSemSim.md index 00000000..567a18bb
mkdocs/mysoftware/ReactomePA.md index 00000000..066e12c3
mkdocs/mysoftware/clusterProfiler.md index 00000000..8f693689
mkdocs/mysoftware/emojifont.md index 00000000..9f244a0c
mkdocs/mysoftware/ggtree.md index 00000000..f7923cdd
mkdocs/mysoftware/meshes.md index 00000000..c6797a68
mkdocs/mysoftware/treeio.md index 00000000..e8dfb92b

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docs/featuredArticles/index.html

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@@ -223,11 +223,11 @@
+                       }
                        </style>
                     -<div id = 'chart3e0e14505d80' class = 'rChart morris'></div>
                     +<div id = 'chart43e87111221b' class = 'rChart morris'></div>
                      <script type='text/javascript'>
                          var chartParams = {
                     - "element": "chart3e0e14505d80",
                     + "element": "chart43e87111221b",
                      "width":            800,
                      "height":            400,
                      "xkey": "year",
@@ -241,7 +241,7 @@
                      "pubid": "HtEfBTGE9r8C"
+                     }
                      ],
                     -"id": "chart3e0e14505d80",
                     +"id": "chart43e87111221b",
                      "labels": "cites"
                      },
                            chartType = "Bar"

docs/mkdocs/search_index.json

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@@ -207,7 +207,7 @@
         }, 
         {
             "location": "/featuredArticles/", 
-            "text": "Let us know\n if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart3e0e14505d80\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart3e0e14505d80\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape\n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens\n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015\n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species\n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976", 
+            "text": "Let us know\n if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart43e87111221b\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart43e87111221b\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape\n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens\n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015\n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species\n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976", 
             "title": "Featured Articles"
         }, 
         {

mkdocs/docs/featuredArticles.md

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@@ -36,10 +36,10 @@
+                       }
                        </style>
                     -<div id = 'chart3e0e14505d80' class = 'rChart morris'></div>
                     +<div id = 'chart43e87111221b' class = 'rChart morris'></div>
                      <script type='text/javascript'>
                          var chartParams = {
                     - "element": "chart3e0e14505d80",
                     + "element": "chart43e87111221b",
                      "width":            800,
                      "height":            400,
                      "xkey": "year",
@@ -53,7 +53,7 @@
                      "pubid": "HtEfBTGE9r8C"
+                     }
                      ],
                     -"id": "chart3e0e14505d80",
                     +"id": "chart43e87111221b",
                      "labels": "cites"
                      },
                            chartType = "Bar"

mkdocs/mysoftware

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                     deleted file mode 160000
@@ -1 +0,0 @@
                     -Subproject commit bfcc3e40cd37c36c34ec94101effedfa165151d0

mkdocs/mysoftware/ChIPseeker.md

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                     new file mode 100644
@@ -0,0 +1 @@
                     +<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/ChIPseeker" />

mkdocs/mysoftware/DOSE.md

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                     new file mode 100644
@@ -0,0 +1 @@
                     +<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/DOSE" />

mkdocs/mysoftware/GOSemSim.md

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                     new file mode 100644
@@ -0,0 +1 @@
                     +<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/GOSemSim" />

mkdocs/mysoftware/ReactomePA.md

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                     new file mode 100644
@@ -0,0 +1 @@
                     +<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/ReactomePA" />

mkdocs/mysoftware/clusterProfiler.md

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                     new file mode 100644
@@ -0,0 +1 @@
                     +<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/clusterProfiler" />

mkdocs/mysoftware/emojifont.md

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                     new file mode 100644
@@ -0,0 +1 @@
                     +<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/emojifont" />

mkdocs/mysoftware/ggtree.md

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                     new file mode 100644
@@ -0,0 +1 @@
                     +<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/ggtree" />

mkdocs/mysoftware/meshes.md

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                     new file mode 100644
@@ -0,0 +1 @@
                     +<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/meshes" />

mkdocs/mysoftware/treeio.md

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                     new file mode 100644
@@ -0,0 +1 @@
                     +<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/treeio" />

...	...	@@ -207,7 +207,7 @@
207	207	},
208	208	{
209	209	"location": "/featuredArticles/",
210		- "text": "Let us know\n if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n .rChart {\n display: block;\n margin-left: auto; \n margin-right: auto;\n width: 800px;\n height: 300px;\n } \n \n\n\n\n\n\n\n\n var chartParams = {\n \"element\": \"chart3e0e14505d80\",\n\"width\": 800,\n\"height\": 400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\": 1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart3e0e14505d80\",\n\"labels\": \"cites\" \n},\n chartType = \"Bar\"\n new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape\n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens\n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015\n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species\n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976",
	210	+ "text": "Let us know\n if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n .rChart {\n display: block;\n margin-left: auto; \n margin-right: auto;\n width: 800px;\n height: 300px;\n } \n \n\n\n\n\n\n\n\n var chartParams = {\n \"element\": \"chart43e87111221b\",\n\"width\": 800,\n\"height\": 400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\": 1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart43e87111221b\",\n\"labels\": \"cites\" \n},\n chartType = \"Bar\"\n new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape\n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens\n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015\n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species\n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976",
211	211	"title": "Featured Articles"
212	212	},
213	213	{