deleted file mode 100644

@@ -1,37 +0,0 @@

-## reference: http://docs.travis-ci.com/user/languages/r/

-

-language: r

-r:

-  - bioc-devel

-  

-cache: packages

-bioc_required: true

-

-os:

-  - linux

-  - osx

-

-

-apt_packages:

-  - libfftw3-dev

-

-env:

-  global:

-    - _R_CHECK_FORCE_SUGGESTS_=False

-    - R_LIBS="http://cran.rstudio.com"

-

-  

-after_failure:

-  - ./travis-tool.sh dump_logs

-

-r_github_packages:

-  - jimhester/covr

-

-after_success:

-- Rscript -e 'library(covr); codecov()'

-

-## notifications:

-##   email:

-##     on_success: change

-##     on_failure: change

-

deleted file mode 100644

@@ -1,72 +0,0 @@

-PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)

-PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)

-PKGSRC  := $(shell basename `pwd`)

-

-all: rd readme check clean

-

-alldocs: rd readme mkdocs

-

-rd:

-	Rscript -e 'roxygen2::roxygenise(".")'

-

-readme:

-	Rscript -e 'rmarkdown::render("README.Rmd")'

-

-build:

-	cd ..;\

-	R CMD build $(PKGSRC)

-

-build2:

-	cd ..;\

-	R CMD build --no-build-vignettes $(PKGSRC)

-

-install:

-	cd ..;\

-	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz

-

-check: build

-	cd ..;\

-	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'

-

-check2: build

-	cd ..;\

-	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz

-

-bioccheck:

-	cd ..;\

-	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'

-

-clean:

-	cd ..;\

-	$(RM) -r $(PKGNAME).Rcheck/

-

-site: mkdocs

-

-mkdocs: mdfiles

-	cd mkdocs;\

-	mkdocs build;\

-	cd ../docs;\

-	rm -rf fonts;\

-	rm -rf css/font-awesome*

-

-mdfiles:

-	cd mkdocs;\

-	Rscript -e 'library(ypages); gendoc("private/index.md", "blue", "docs/index.md")';\

-	Rscript -e 'library(ypages); gendoc("private/documentation.md", "blue", "docs/documentation.md")';\

-	Rscript -e 'library(ypages); gendoc("private/featuredArticles.md", "blue", "docs/featuredArticles.md")';\

-	Rscript -e 'library(ypages); gendoc("private/faq.md", "blue", "docs/faq.md")';\

-	cd docs;\

-	ln -f -s ../mysoftware/* ./

-

-

-svnignore:

-	svn propset svn:ignore -F .svnignore .

-

-svncommit:

-	git checkout devel;\

-	git svn rebase;\

-	git merge master --log;\

-	git svn dcommit;\

-	git push -u origin devel;\

-	git checkout master;\

-	git merge devel

deleted file mode 100644

@@ -1,86 +0,0 @@

-output:

-  md_document:

-    variant: markdown_github

-html_preview: false

-

-#  ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

-

-```{r echo=FALSE, results="hide", message=FALSE}

-library("txtplot")

-library("ypages")

-```

-

-`r badge_release("ggtree", "green")`

-`r badge_devel("ggtree", "green")`

-[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)

-`r badge_download("ggtree", "total", "blue")`

-`r badge_download("ggtree", "month", "blue")`

-

-

-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)

-[![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)

-[![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

-[![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network)

-[![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)

-[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

-

-[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)

-[![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)

-[![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree)

-[![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)

-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)

-

-

-

-The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.

-

-[![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)

-

-

-Please cite the following article when using `ggtree`:

-

-__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. _accepted_

-

-`r badge_doi("10.1111/2041-210X.12628", "green")`

-`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`

-`r badge_altmetric("10533079", "green")`

-

-

-For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.

-

-+ [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)

-+ [FAQ](https://guangchuangyu.github.io/ggtree/faq/)

-+ [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)

-+ [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)

-

-### Citation

-

-`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`

-

-

-```{r echo=F, comment=NA}

-d <- get_article_cite_history('DO5oG40AAAAJ', 'HtEfBTGE9r8C')

-txtplot(d$year, d$cites, xlim=c(2015, 2017))

-```

-

-### Download stats

-

-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/)

-`r badge_download("ggtree", "total", "blue")`

-`r badge_download("ggtree", "month", "blue")`

-

-

-```{r echo=F, comment=NA}

-x <- dlstats::bioc_stats("ggtree")

-x <- x[-nrow(x), ] # last month data is not complete

-txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25)

-```

-

-

-

-

-

deleted file mode 100644

@@ -1,50 +0,0 @@

-environment:

-  matrix:

-    - R_VERSION: devel

-      R_ARCH: x64

-      USE_RTOOLS: true

-  _R_CHECK_FORCE_SUGGESTS_: false

-

-# DO NOT CHANGE the "init" and "install" sections below

-

-# Download script file from GitHub

-init:

-  ps: |

-        $ErrorActionPreference = "Stop"

-        Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"

-        Import-Module '..\appveyor-tool.ps1'

-

-install:

-  ps: Bootstrap

-

-# Adapt as necessary starting from here

-

-build_script:

-  - travis-tool.sh install_bioc BiocStyle Biostrings  

-  - travis-tool.sh install_deps

-

-test_script:

-  - travis-tool.sh run_tests

-

-on_failure:

-  - 7z a failure.zip *.Rcheck\*

-  - appveyor PushArtifact failure.zip

-

-artifacts:

-  - path: '*.Rcheck\**\*.log'

-    name: Logs

-

-  - path: '*.Rcheck\**\*.out'

-    name: Logs

-

-  - path: '*.Rcheck\**\*.fail'

-    name: Logs

-

-  - path: '*.Rcheck\**\*.Rout'

-    name: Logs

-

-  - path: '\*_*.tar.gz'

-    name: Linux Package

-

-  - path: '\*_*.zip'

-    name: Windows Package

deleted file mode 100644

@@ -1,216 +0,0 @@

-<!DOCTYPE html>

-<html lang="en">

-    <head>

-        <meta charset="utf-8">

-        <meta http-equiv="X-UA-Compatible" content="IE=edge">

-        <meta name="viewport" content="width=device-width, initial-scale=1.0">

-        

-        <meta name="author" content="Guangchuang Yu">

-        <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/ChIPseeker/">

-        <link rel="shortcut icon" href="../img/favicon.ico">

-

-	<title>ChIPseeker - ggtree</title>

-

-        <link href="../css/bootstrap-custom.min.css" rel="stylesheet">

-        <link href="../css/font-awesome-4.0.3.css" rel="stylesheet">

-        <link rel="stylesheet" href="../css/highlight.css">

-        <link href="../css/base.css" rel="stylesheet">

-

-        <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->

-        <!--[if lt IE 9]>

-            <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>

-            <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>

-        <![endif]-->

-

-        

-        <script>

-            (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){

-            (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),

-            m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)

-            })(window,document,'script','//www.google-analytics.com/analytics.js','ga');

-

-            ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');

-            ga('send', 'pageview');

-        </script>

-        

-    </head>

-

-    <body>

-

-        <div class="navbar navbar-default navbar-fixed-top" role="navigation">

-    <div class="container">

-

-        <!-- Collapsed navigation -->

-        <div class="navbar-header">

-            <!-- Expander button -->

-            <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">

-                <span class="sr-only">Toggle navigation</span>

-                <span class="icon-bar"></span>

-                <span class="icon-bar"></span>

-                <span class="icon-bar"></span>

-            </button>

-

-            <!-- Main title -->

-            <a class="navbar-brand" href="..">ggtree</a>

-        </div>

-

-        <!-- Expanded navigation -->

-        <div class="navbar-collapse collapse">

-            <!-- Main navigation -->

-            <ul class="nav navbar-nav">

-            

-            

-                <li >

-                    <a href="..">Home</a>

-                </li>

-            

-            

-            

-                <li >

-                    <a href="../documentation/">Documentation</a>

-                </li>

-            

-            

-            

-                <li >

-                    <a href="../faq/">FAQ</a>

-                </li>

-            

-            

-            

-                <li >

-                    <a href="../featuredArticles/">Featured Articles</a>

-                </li>

-            

-            

-            

-                <li class="dropdown active">

-                    <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>

-                    <ul class="dropdown-menu">

-                    

-                        

-<li class="active">

-    <a href="./">ChIPseeker</a>

-</li>

-

-                    

-                        

-<li >

-    <a href="../clusterProfiler/">clusterProfiler</a>

-</li>

-

-                    

-                        

-<li >

-    <a href="../DOSE/">DOSE</a>

-</li>

-

-                    

-                        

-<li >

-    <a href="../ggtree/">ggtree</a>

-</li>

-

-                    

-                        

-<li >

-    <a href="../GOSemSim/">GOSemSim</a>

-</li>

-

-                    

-                        

-<li >

-    <a href="../ReactomePA/">ReactomePA</a>

-</li>

-

-                    

-                    </ul>

-                </li>

-            

-            

-            </ul>

-

-            <!-- Search, Navigation and Repo links -->

-            <ul class="nav navbar-nav navbar-right">

-                <li>

-                    <a href="#" data-toggle="modal" data-target="#mkdocs_search_modal">

-                        <i class="fa fa-search"></i> Search

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-                <li >

-                    <a rel="next" href="../featuredArticles/">

-                        <i class="fa fa-arrow-left"></i> Previous

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-                </li>

-                <li >

-                    <a rel="prev" href="../clusterProfiler/">

-                        Next <i class="fa fa-arrow-right"></i>

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-                        

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-                

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-        </div>

-    </div>

-</div>

-

-        <div class="container">

-            <div class="col-md-3"><div class="bs-sidebar hidden-print affix well" role="complementary">

-    <ul class="nav bs-sidenav">

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-        </div>

-

-        <footer class="col-md-12">

-            <hr>

-            

-                <center>Copyright &copy; 2016 <a href="https://guangchuangyu.github.io">Guangchuang Yu</a>.<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div></center>

-            

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-        </footer>

-

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-        <script src="../js/bootstrap-3.0.3.min.js"></script>

-        <script src="../js/highlight.pack.js"></script>

-        <script>var base_url = '..';</script>

-        <script data-main="../mkdocs/js/search.js" src="../mkdocs/js/require.js"></script>

-        <script src="../js/base.js"></script>

-

-        <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true">

-            <div class="modal-dialog">

-                <div class="modal-content">

-                    <div class="modal-header">

-                        <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button>

-                        <h4 class="modal-title" id="exampleModalLabel">Search</h4>

-                    </div>

-                    <div class="modal-body">

-                        <p>

-                            From here you can search these documents. Enter

-                            your search terms below.

-                        </p>

-                        <form role="form">

-                            <div class="form-group">

-                                <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query">

-                            </div>

-                        </form>

-                        <div id="mkdocs-search-results"></div>

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-                </div>

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-    </body>

-</html>

\ No newline at end of file

deleted file mode 100644

@@ -1,216 +0,0 @@

-<!DOCTYPE html>

-<html lang="en">

-    <head>

-        <meta charset="utf-8">

-        <meta http-equiv="X-UA-Compatible" content="IE=edge">

-        <meta name="viewport" content="width=device-width, initial-scale=1.0">

-        

-        <meta name="author" content="Guangchuang Yu">

-        <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/DOSE/">

-        <link rel="shortcut icon" href="../img/favicon.ico">

-

-	<title>DOSE - ggtree</title>

-

-        <link href="../css/bootstrap-custom.min.css" rel="stylesheet">

-        <link href="../css/font-awesome-4.0.3.css" rel="stylesheet">

-        <link rel="stylesheet" href="../css/highlight.css">

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-            })(window,document,'script','//www.google-analytics.com/analytics.js','ga');

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-        </div>

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-            <!-- Main navigation -->

-            <ul class="nav navbar-nav">

-            

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-                <li >

-                    <a href="..">Home</a>

-                </li>

-            

-            

-            

-                <li >

-                    <a href="../documentation/">Documentation</a>

-                </li>

-            

-            

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-                <li >

-                    <a href="../faq/">FAQ</a>

-                </li>

-            

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-            

-                <li >

-                    <a href="../featuredArticles/">Featured Articles</a>

-                </li>

-            

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-            

-                <li class="dropdown active">

-                    <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>

-                    <ul class="dropdown-menu">

-                    

-                        

-<li >

-    <a href="../ChIPseeker/">ChIPseeker</a>

-</li>

-

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-                        

-<li >

-    <a href="../clusterProfiler/">clusterProfiler</a>

-</li>

-

-                    

-                        

-<li class="active">

-    <a href="./">DOSE</a>

-</li>

-

-                    

-                        

-<li >

-    <a href="../ggtree/">ggtree</a>

-</li>

-

-                    

-                        

-<li >

-    <a href="../GOSemSim/">GOSemSim</a>

-</li>

-

-                    

-                        

-<li >

-    <a href="../ReactomePA/">ReactomePA</a>

-</li>

-

-                    

-                    </ul>

-                </li>

-            

-            

-            </ul>

-

-            <!-- Search, Navigation and Repo links -->

-            <ul class="nav navbar-nav navbar-right">

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-                    <a href="#" data-toggle="modal" data-target="#mkdocs_search_modal">

-                        <i class="fa fa-search"></i> Search

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-                        <i class="fa fa-arrow-left"></i> Previous

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-                        Next <i class="fa fa-arrow-right"></i>

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-        <script src="../js/base.js"></script>

-

-        <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true">

-            <div class="modal-dialog">

-                <div class="modal-content">

-                    <div class="modal-header">

-                        <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button>

-                        <h4 class="modal-title" id="exampleModalLabel">Search</h4>

-                    </div>

-                    <div class="modal-body">

-                        <p>

-                            From here you can search these documents. Enter

-                            your search terms below.

-                        </p>

-                        <form role="form">

-                            <div class="form-group">

-                                <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query">

-                            </div>

-                        </form>

-                        <div id="mkdocs-search-results"></div>

-                    </div>

-                    <div class="modal-footer">

-                    </div>

-                </div>

-            </div>

-        </div>

-    </body>

-</html>

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-<!DOCTYPE html>

-<html lang="en">

-    <head>

-        <meta charset="utf-8">

-        <meta http-equiv="X-UA-Compatible" content="IE=edge">

-        <meta name="viewport" content="width=device-width, initial-scale=1.0">

-        

-        <meta name="author" content="Guangchuang Yu">

-        <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/GOSemSim/">

-        <link rel="shortcut icon" href="../img/favicon.ico">

-

-	<title>GOSemSim - ggtree</title>

-

-        <link href="../css/bootstrap-custom.min.css" rel="stylesheet">

-        <link href="../css/font-awesome-4.0.3.css" rel="stylesheet">

-        <link rel="stylesheet" href="../css/highlight.css">

-        <link href="../css/base.css" rel="stylesheet">

-

-        <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->

-        <!--[if lt IE 9]>

-            <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>

-            <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>

-        <![endif]-->

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-        

-        <script>

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-            })(window,document,'script','//www.google-analytics.com/analytics.js','ga');

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-            ga('send', 'pageview');

-        </script>

-        

-    </head>

-

-    <body>

-

-        <div class="navbar navbar-default navbar-fixed-top" role="navigation">

-    <div class="container">

-

-        <!-- Collapsed navigation -->

-        <div class="navbar-header">

-            <!-- Expander button -->

-            <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">

-                <span class="sr-only">Toggle navigation</span>

-                <span class="icon-bar"></span>

-                <span class="icon-bar"></span>

-                <span class="icon-bar"></span>

-            </button>

-

-            <!-- Main title -->

-            <a class="navbar-brand" href="..">ggtree</a>

-        </div>

-

-        <!-- Expanded navigation -->

-        <div class="navbar-collapse collapse">

-            <!-- Main navigation -->

-            <ul class="nav navbar-nav">

-            

-            

-                <li >

-                    <a href="..">Home</a>

-                </li>

-            

-            

-            

-                <li >

-                    <a href="../documentation/">Documentation</a>

-                </li>

-            

-            

-            

-                <li >

-                    <a href="../faq/">FAQ</a>

-                </li>

-            

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-                <li >

-                    <a href="../featuredArticles/">Featured Articles</a>

-                </li>

-            

-            

-            

-                <li class="dropdown active">

-                    <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>

-                    <ul class="dropdown-menu">

-                    

-                        

-<li >

-    <a href="../ChIPseeker/">ChIPseeker</a>

-</li>

-

-                    

-                        

-<li >

-    <a href="../clusterProfiler/">clusterProfiler</a>

-</li>

-

-                    

-                        

-<li >

-    <a href="../DOSE/">DOSE</a>

-</li>

-

-                    

-                        

-<li >

-    <a href="../ggtree/">ggtree</a>

-</li>

-

-                    

-                        

-<li class="active">

-    <a href="./">GOSemSim</a>

-</li>

-

-                    

-                        

-<li >

-    <a href="../ReactomePA/">ReactomePA</a>

-</li>

-

-                    

-                    </ul>

-                </li>

-            

-            

-            </ul>

-

-            <!-- Search, Navigation and Repo links -->

-            <ul class="nav navbar-nav navbar-right">

-                <li>

-                    <a href="#" data-toggle="modal" data-target="#mkdocs_search_modal">

-                        <i class="fa fa-search"></i> Search

-                    </a>

-                </li>

-                <li >

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-                        <i class="fa fa-arrow-left"></i> Previous

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-                        

-                        GitHub

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-                </li>

-                

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-        </div>

-    </div>

-</div>

-