git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122176 bc3139a8-67e5-0310-9ffc-ced21a209358
Guangchuang Yu authored on 11/10/2016 02:10:31
| 18 | 11 |
new file mode 100644 |
| ... | ... |
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+PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION) |
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| 2 |
+PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION) |
|
| 3 |
+PKGSRC := $(shell basename `pwd`) |
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| 4 |
+ |
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| 5 |
+all: rd readme check clean |
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| 6 |
+ |
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| 7 |
+alldocs: rd readme mkdocs |
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| 8 |
+ |
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| 9 |
+rd: |
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| 10 |
+ Rscript -e 'roxygen2::roxygenise(".")'
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| 11 |
+ |
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| 12 |
+readme: |
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| 13 |
+ Rscript -e 'rmarkdown::render("README.Rmd")'
|
|
| 14 |
+ |
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| 15 |
+build: |
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| 16 |
+ cd ..;\ |
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| 17 |
+ R CMD build $(PKGSRC) |
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+ |
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+build2: |
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| 20 |
+ cd ..;\ |
|
| 21 |
+ R CMD build --no-build-vignettes $(PKGSRC) |
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| 22 |
+ |
|
| 23 |
+install: |
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| 24 |
+ cd ..;\ |
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| 25 |
+ R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz |
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+ |
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| 27 |
+check: build |
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+ cd ..;\ |
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| 29 |
+ Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
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+ |
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+check2: build |
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+ cd ..;\ |
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+ R CMD check $(PKGNAME)_$(PKGVERS).tar.gz |
|
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+ |
|
| 35 |
+bioccheck: |
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| 36 |
+ cd ..;\ |
|
| 37 |
+ Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
|
|
| 38 |
+ |
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+clean: |
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| 40 |
+ cd ..;\ |
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| 41 |
+ $(RM) -r $(PKGNAME).Rcheck/ |
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+ |
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| 43 |
+site: mkdocs |
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+ |
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+mkdocs: mdfiles |
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+ cd mkdocs;\ |
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| 47 |
+ mkdocs build;\ |
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+ cd ../docs;\ |
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| 49 |
+ rm -rf fonts;\ |
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| 50 |
+ rm -rf css/font-awesome* |
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| 51 |
+ |
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| 52 |
+mdfiles: |
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+ cd mkdocs;\ |
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| 54 |
+ Rscript -e 'library(ypages); gendoc("private/index.md", "blue", "docs/index.md")';\
|
|
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+ Rscript -e 'library(ypages); gendoc("private/documentation.md", "blue", "docs/documentation.md")';\
|
|
| 56 |
+ Rscript -e 'library(ypages); gendoc("private/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
|
|
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+ Rscript -e 'library(ypages); gendoc("private/faq.md", "blue", "docs/faq.md")';\
|
|
| 58 |
+ cd docs;\ |
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+ ln -f -s ../mysoftware/* ./ |
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+ |
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+ |
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+svnignore: |
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| 63 |
+ svn propset svn:ignore -F .svnignore . |
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+ |
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+svncommit: |
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+ git checkout devel;\ |
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+ git svn rebase;\ |
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+ git merge master --log;\ |
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+ git svn dcommit;\ |
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+ git checkout master;\ |
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+ git merge devel |
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new file mode 100644 |
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+--- |
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| 2 |
+output: |
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+ md_document: |
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| 4 |
+ variant: markdown_github |
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| 5 |
+html_preview: false |
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| 6 |
+--- |
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+ |
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| 8 |
+# ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data |
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| 9 |
+ |
|
| 10 |
+```{r echo=FALSE, results="hide", message=FALSE}
|
|
| 11 |
+library("txtplot")
|
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+library("ypages")
|
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| 13 |
+``` |
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| 14 |
+ |
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| 15 |
+`r badge_release("ggtree", "green")`
|
|
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+`r badge_devel("ggtree", "green")`
|
|
| 17 |
+[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) |
|
| 18 |
+`r badge_download("ggtree", "total", "blue")`
|
|
| 19 |
+`r badge_download("ggtree", "month", "blue")`
|
|
| 20 |
+ |
|
| 21 |
+ |
|
| 22 |
+[](http://www.repostatus.org/#active) |
|
| 23 |
+[](https://codecov.io/gh/GuangchuangYu/ggtree) |
|
| 24 |
+[)`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
|
|
| 25 |
+[](https://github.com/GuangchuangYu/ggtree/network) |
|
| 26 |
+[](https://github.com/GuangchuangYu/ggtree/stargazers) |
|
| 27 |
+[](https://awesome-r.com/#awesome-r-graphic-displays) |
|
| 28 |
+ |
|
| 29 |
+[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) |
|
| 30 |
+[](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) |
|
| 31 |
+[](https://travis-ci.org/GuangchuangYu/ggtree) |
|
| 32 |
+[](https://ci.appveyor.com/project/GuangchuangYu/ggtree) |
|
| 33 |
+[](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html) |
|
| 34 |
+ |
|
| 35 |
+ |
|
| 36 |
+ |
|
| 37 |
+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. |
|
| 38 |
+ |
|
| 39 |
+[](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu) |
|
| 40 |
+ |
|
| 41 |
+----------------------------------------------------- |
|
| 42 |
+ |
|
| 43 |
+Please cite the following article when using `ggtree`: |
|
| 44 |
+ |
|
| 45 |
+__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_ |
|
| 46 |
+ |
|
| 47 |
+`r badge_doi("10.1111/2041-210X.12628", "green")`
|
|
| 48 |
+`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
|
|
| 49 |
+`r badge_altmetric("10533079", "green")`
|
|
| 50 |
+ |
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| 51 |
+---------------------------------------------------------------------------------------- |
|
| 52 |
+ |
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| 53 |
+For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>. |
|
| 54 |
+ |
|
| 55 |
++ [Documentation](https://guangchuangyu.github.io/ggtree/documentation/) |
|
| 56 |
++ [FAQ](https://guangchuangyu.github.io/ggtree/faq/) |
|
| 57 |
++ [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/) |
|
| 58 |
++ [Feedback](https://guangchuangyu.github.io/ggtree/#feedback) |
|
| 59 |
+ |
|
| 60 |
+### Citation |
|
| 61 |
+ |
|
| 62 |
+`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
|
|
| 63 |
+ |
|
| 64 |
+ |
|
| 65 |
+```{r echo=F, comment=NA}
|
|
| 66 |
+d <- get_article_cite_history('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
|
|
| 67 |
+txtplot(d$year, d$cites, xlim=c(2015, 2017)) |
|
| 68 |
+``` |
|
| 69 |
+ |
|
| 70 |
+### Download stats |
|
| 71 |
+ |
|
| 72 |
+[](https://bioconductor.org/packages/stats/bioc/ggtree/) |
|
| 73 |
+`r badge_download("ggtree", "total", "blue")`
|
|
| 74 |
+`r badge_download("ggtree", "month", "blue")`
|
|
| 75 |
+ |
|
| 76 |
+ |
|
| 77 |
+```{r echo=F, comment=NA}
|
|
| 78 |
+x <- dlstats::bioc_stats("ggtree")
|
|
| 79 |
+x <- x[-nrow(x), ] # last month data is not complete |
|
| 80 |
+txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25) |
|
| 81 |
+``` |
|
| 82 |
+ |
|
| 83 |
+ |
|
| 84 |
+ |
|
| 85 |
+ |
|
| 86 |
+ |
| 0 | 87 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,12 @@ |
| 1 |
++ attach user specific data to existing tree object |
|
| 2 |
++ attach user specific data by node number |
|
| 3 |
++ mask function that accepts tree object, feature name and a function that specific how to mask. |
|
| 4 |
+ with this function, user can mask some of the features that are not needed to display on a tree. |
|
| 5 |
++ defined a function, compare_sequence, that accept a function that defined sequence feature, |
|
| 6 |
+ and compare the feature from parent to children and add store the info in tree object. |
|
| 7 |
+ So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison, |
|
| 8 |
+ not only substitution supported internally. |
|
| 9 |
++ support more features that can be plotted at the right hand side of the tree. |
|
| 10 |
+ - ~~multiple sequence alignment~~ _Now implemented in 1.1.7_ |
|
| 11 |
+ |
|
| 12 |
+ |
| 0 | 13 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,50 @@ |
| 1 |
+environment: |
|
| 2 |
+ matrix: |
|
| 3 |
+ - R_VERSION: devel |
|
| 4 |
+ R_ARCH: x64 |
|
| 5 |
+ USE_RTOOLS: true |
|
| 6 |
+ _R_CHECK_FORCE_SUGGESTS_: false |
|
| 7 |
+ |
|
| 8 |
+# DO NOT CHANGE the "init" and "install" sections below |
|
| 9 |
+ |
|
| 10 |
+# Download script file from GitHub |
|
| 11 |
+init: |
|
| 12 |
+ ps: | |
|
| 13 |
+ $ErrorActionPreference = "Stop" |
|
| 14 |
+ Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" |
|
| 15 |
+ Import-Module '..\appveyor-tool.ps1' |
|
| 16 |
+ |
|
| 17 |
+install: |
|
| 18 |
+ ps: Bootstrap |
|
| 19 |
+ |
|
| 20 |
+# Adapt as necessary starting from here |
|
| 21 |
+ |
|
| 22 |
+build_script: |
|
| 23 |
+ - travis-tool.sh install_bioc BiocStyle Biostrings |
|
| 24 |
+ - travis-tool.sh install_deps |
|
| 25 |
+ |
|
| 26 |
+test_script: |
|
| 27 |
+ - travis-tool.sh run_tests |
|
| 28 |
+ |
|
| 29 |
+on_failure: |
|
| 30 |
+ - 7z a failure.zip *.Rcheck\* |
|
| 31 |
+ - appveyor PushArtifact failure.zip |
|
| 32 |
+ |
|
| 33 |
+artifacts: |
|
| 34 |
+ - path: '*.Rcheck\**\*.log' |
|
| 35 |
+ name: Logs |
|
| 36 |
+ |
|
| 37 |
+ - path: '*.Rcheck\**\*.out' |
|
| 38 |
+ name: Logs |
|
| 39 |
+ |
|
| 40 |
+ - path: '*.Rcheck\**\*.fail' |
|
| 41 |
+ name: Logs |
|
| 42 |
+ |
|
| 43 |
+ - path: '*.Rcheck\**\*.Rout' |
|
| 44 |
+ name: Logs |
|
| 45 |
+ |
|
| 46 |
+ - path: '\*_*.tar.gz' |
|
| 47 |
+ name: Linux Package |
|
| 48 |
+ |
|
| 49 |
+ - path: '\*_*.zip' |
|
| 50 |
+ name: Windows Package |
| 0 | 51 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,216 @@ |
| 1 |
+<!DOCTYPE html> |
|
| 2 |
+<html lang="en"> |
|
| 3 |
+ <head> |
|
| 4 |
+ <meta charset="utf-8"> |
|
| 5 |
+ <meta http-equiv="X-UA-Compatible" content="IE=edge"> |
|
| 6 |
+ <meta name="viewport" content="width=device-width, initial-scale=1.0"> |
|
| 7 |
+ |
|
| 8 |
+ <meta name="author" content="Guangchuang Yu"> |
|
| 9 |
+ <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/ChIPseeker/"> |
|
| 10 |
+ <link rel="shortcut icon" href="../img/favicon.ico"> |
|
| 11 |
+ |
|
| 12 |
+ <title>ChIPseeker - ggtree</title> |
|
| 13 |
+ |
|
| 14 |
+ <link href="../css/bootstrap-custom.min.css" rel="stylesheet"> |
|
| 15 |
+ <link href="../css/font-awesome-4.0.3.css" rel="stylesheet"> |
|
| 16 |
+ <link rel="stylesheet" href="../css/highlight.css"> |
|
| 17 |
+ <link href="../css/base.css" rel="stylesheet"> |
|
| 18 |
+ |
|
| 19 |
+ <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries --> |
|
| 20 |
+ <!--[if lt IE 9]> |
|
| 21 |
+ <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script> |
|
| 22 |
+ <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script> |
|
| 23 |
+ <![endif]--> |
|
| 24 |
+ |
|
| 25 |
+ |
|
| 26 |
+ <script> |
|
| 27 |
+ (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
|
|
| 28 |
+ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), |
|
| 29 |
+ m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) |
|
| 30 |
+ })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); |
|
| 31 |
+ |
|
| 32 |
+ ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');
|
|
| 33 |
+ ga('send', 'pageview');
|
|
| 34 |
+ </script> |
|
| 35 |
+ |
|
| 36 |
+ </head> |
|
| 37 |
+ |
|
| 38 |
+ <body> |
|
| 39 |
+ |
|
| 40 |
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> |
|
| 41 |
+ <div class="container"> |
|
| 42 |
+ |
|
| 43 |
+ <!-- Collapsed navigation --> |
|
| 44 |
+ <div class="navbar-header"> |
|
| 45 |
+ <!-- Expander button --> |
|
| 46 |
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse"> |
|
| 47 |
+ <span class="sr-only">Toggle navigation</span> |
|
| 48 |
+ <span class="icon-bar"></span> |
|
| 49 |
+ <span class="icon-bar"></span> |
|
| 50 |
+ <span class="icon-bar"></span> |
|
| 51 |
+ </button> |
|
| 52 |
+ |
|
| 53 |
+ <!-- Main title --> |
|
| 54 |
+ <a class="navbar-brand" href="..">ggtree</a> |
|
| 55 |
+ </div> |
|
| 56 |
+ |
|
| 57 |
+ <!-- Expanded navigation --> |
|
| 58 |
+ <div class="navbar-collapse collapse"> |
|
| 59 |
+ <!-- Main navigation --> |
|
| 60 |
+ <ul class="nav navbar-nav"> |
|
| 61 |
+ |
|
| 62 |
+ |
|
| 63 |
+ <li > |
|
| 64 |
+ <a href="..">Home</a> |
|
| 65 |
+ </li> |
|
| 66 |
+ |
|
| 67 |
+ |
|
| 68 |
+ |
|
| 69 |
+ <li > |
|
| 70 |
+ <a href="../documentation/">Documentation</a> |
|
| 71 |
+ </li> |
|
| 72 |
+ |
|
| 73 |
+ |
|
| 74 |
+ |
|
| 75 |
+ <li > |
|
| 76 |
+ <a href="../faq/">FAQ</a> |
|
| 77 |
+ </li> |
|
| 78 |
+ |
|
| 79 |
+ |
|
| 80 |
+ |
|
| 81 |
+ <li > |
|
| 82 |
+ <a href="../featuredArticles/">Featured Articles</a> |
|
| 83 |
+ </li> |
|
| 84 |
+ |
|
| 85 |
+ |
|
| 86 |
+ |
|
| 87 |
+ <li class="dropdown active"> |
|
| 88 |
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a> |
|
| 89 |
+ <ul class="dropdown-menu"> |
|
| 90 |
+ |
|
| 91 |
+ |
|
| 92 |
+<li class="active"> |
|
| 93 |
+ <a href="./">ChIPseeker</a> |
|
| 94 |
+</li> |
|
| 95 |
+ |
|
| 96 |
+ |
|
| 97 |
+ |
|
| 98 |
+<li > |
|
| 99 |
+ <a href="../clusterProfiler/">clusterProfiler</a> |
|
| 100 |
+</li> |
|
| 101 |
+ |
|
| 102 |
+ |
|
| 103 |
+ |
|
| 104 |
+<li > |
|
| 105 |
+ <a href="../DOSE/">DOSE</a> |
|
| 106 |
+</li> |
|
| 107 |
+ |
|
| 108 |
+ |
|
| 109 |
+ |
|
| 110 |
+<li > |
|
| 111 |
+ <a href="../ggtree/">ggtree</a> |
|
| 112 |
+</li> |
|
| 113 |
+ |
|
| 114 |
+ |
|
| 115 |
+ |
|
| 116 |
+<li > |
|
| 117 |
+ <a href="../GOSemSim/">GOSemSim</a> |
|
| 118 |
+</li> |
|
| 119 |
+ |
|
| 120 |
+ |
|
| 121 |
+ |
|
| 122 |
+<li > |
|
| 123 |
+ <a href="../ReactomePA/">ReactomePA</a> |
|
| 124 |
+</li> |
|
| 125 |
+ |
|
| 126 |
+ |
|
| 127 |
+ </ul> |
|
| 128 |
+ </li> |
|
| 129 |
+ |
|
| 130 |
+ |
|
| 131 |
+ </ul> |
|
| 132 |
+ |
|
| 133 |
+ <!-- Search, Navigation and Repo links --> |
|
| 134 |
+ <ul class="nav navbar-nav navbar-right"> |
|
| 135 |
+ <li> |
|
| 136 |
+ <a href="#" data-toggle="modal" data-target="#mkdocs_search_modal"> |
|
| 137 |
+ <i class="fa fa-search"></i> Search |
|
| 138 |
+ </a> |
|
| 139 |
+ </li> |
|
| 140 |
+ <li > |
|
| 141 |
+ <a rel="next" href="../featuredArticles/"> |
|
| 142 |
+ <i class="fa fa-arrow-left"></i> Previous |
|
| 143 |
+ </a> |
|
| 144 |
+ </li> |
|
| 145 |
+ <li > |
|
| 146 |
+ <a rel="prev" href="../clusterProfiler/"> |
|
| 147 |
+ Next <i class="fa fa-arrow-right"></i> |
|
| 148 |
+ </a> |
|
| 149 |
+ </li> |
|
| 150 |
+ |
|
| 151 |
+ <li> |
|
| 152 |
+ <a href="https://github.com/GuangchuangYu/ggtree"> |
|
| 153 |
+ |
|
| 154 |
+ <i class="fa fa-github"></i> |
|
| 155 |
+ |
|
| 156 |
+ GitHub |
|
| 157 |
+ </a> |
|
| 158 |
+ </li> |
|
| 159 |
+ |
|
| 160 |
+ </ul> |
|
| 161 |
+ </div> |
|
| 162 |
+ </div> |
|
| 163 |
+</div> |
|
| 164 |
+ |
|
| 165 |
+ <div class="container"> |
|
| 166 |
+ <div class="col-md-3"><div class="bs-sidebar hidden-print affix well" role="complementary"> |
|
| 167 |
+ <ul class="nav bs-sidenav"> |
|
| 168 |
+ |
|
| 169 |
+ </ul> |
|
| 170 |
+</div></div> |
|
| 171 |
+ <div class="col-md-9" role="main"> |
|
| 172 |
+ |
|
| 173 |
+<p><meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/ChIPseeker" /></p></div> |
|
| 174 |
+ </div> |
|
| 175 |
+ |
|
| 176 |
+ <footer class="col-md-12"> |
|
| 177 |
+ <hr> |
|
| 178 |
+ |
|
| 179 |
+ <center>Copyright © 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&m=0&c=ff0000&cr1=ffffff&sx=0" async="async"></script></div></center> |
|
| 180 |
+ |
|
| 181 |
+ <center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center> |
|
| 182 |
+ </footer> |
|
| 183 |
+ |
|
| 184 |
+ <script src="../js/jquery-1.10.2.min.js"></script> |
|
| 185 |
+ <script src="../js/bootstrap-3.0.3.min.js"></script> |
|
| 186 |
+ <script src="../js/highlight.pack.js"></script> |
|
| 187 |
+ <script>var base_url = '..';</script> |
|
| 188 |
+ <script data-main="../mkdocs/js/search.js" src="../mkdocs/js/require.js"></script> |
|
| 189 |
+ <script src="../js/base.js"></script> |
|
| 190 |
+ |
|
| 191 |
+ <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true"> |
|
| 192 |
+ <div class="modal-dialog"> |
|
| 193 |
+ <div class="modal-content"> |
|
| 194 |
+ <div class="modal-header"> |
|
| 195 |
+ <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">×</span><span class="sr-only">Close</span></button> |
|
| 196 |
+ <h4 class="modal-title" id="exampleModalLabel">Search</h4> |
|
| 197 |
+ </div> |
|
| 198 |
+ <div class="modal-body"> |
|
| 199 |
+ <p> |
|
| 200 |
+ From here you can search these documents. Enter |
|
| 201 |
+ your search terms below. |
|
| 202 |
+ </p> |
|
| 203 |
+ <form role="form"> |
|
| 204 |
+ <div class="form-group"> |
|
| 205 |
+ <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query"> |
|
| 206 |
+ </div> |
|
| 207 |
+ </form> |
|
| 208 |
+ <div id="mkdocs-search-results"></div> |
|
| 209 |
+ </div> |
|
| 210 |
+ <div class="modal-footer"> |
|
| 211 |
+ </div> |
|
| 212 |
+ </div> |
|
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+ </div> |
|
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+ </div> |
|
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+ </body> |
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+</html> |
|
| 0 | 217 |
\ No newline at end of file |
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new file mode 100644 |
| ... | ... |
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| 1 |
+<!DOCTYPE html> |
|
| 2 |
+<html lang="en"> |
|
| 3 |
+ <head> |
|
| 4 |
+ <meta charset="utf-8"> |
|
| 5 |
+ <meta http-equiv="X-UA-Compatible" content="IE=edge"> |
|
| 6 |
+ <meta name="viewport" content="width=device-width, initial-scale=1.0"> |
|
| 7 |
+ |
|
| 8 |
+ <meta name="author" content="Guangchuang Yu"> |
|
| 9 |
+ <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/DOSE/"> |
|
| 10 |
+ <link rel="shortcut icon" href="../img/favicon.ico"> |
|
| 11 |
+ |
|
| 12 |
+ <title>DOSE - ggtree</title> |
|
| 13 |
+ |
|
| 14 |
+ <link href="../css/bootstrap-custom.min.css" rel="stylesheet"> |
|
| 15 |
+ <link href="../css/font-awesome-4.0.3.css" rel="stylesheet"> |
|
| 16 |
+ <link rel="stylesheet" href="../css/highlight.css"> |
|
| 17 |
+ <link href="../css/base.css" rel="stylesheet"> |
|
| 18 |
+ |
|
| 19 |
+ <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries --> |
|
| 20 |
+ <!--[if lt IE 9]> |
|
| 21 |
+ <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script> |
|
| 22 |
+ <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script> |
|
| 23 |
+ <![endif]--> |
|
| 24 |
+ |
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| 25 |
+ |
|
| 26 |
+ <script> |
|
| 27 |
+ (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
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|
| 28 |
+ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), |
|
| 29 |
+ m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) |
|
| 30 |
+ })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); |
|
| 31 |
+ |
|
| 32 |
+ ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');
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|
| 33 |
+ ga('send', 'pageview');
|
|
| 34 |
+ </script> |
|
| 35 |
+ |
|
| 36 |
+ </head> |
|
| 37 |
+ |
|
| 38 |
+ <body> |
|
| 39 |
+ |
|
| 40 |
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> |
|
| 41 |
+ <div class="container"> |
|
| 42 |
+ |
|
| 43 |
+ <!-- Collapsed navigation --> |
|
| 44 |
+ <div class="navbar-header"> |
|
| 45 |
+ <!-- Expander button --> |
|
| 46 |
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse"> |
|
| 47 |
+ <span class="sr-only">Toggle navigation</span> |
|
| 48 |
+ <span class="icon-bar"></span> |
|
| 49 |
+ <span class="icon-bar"></span> |
|
| 50 |
+ <span class="icon-bar"></span> |
|
| 51 |
+ </button> |
|
| 52 |
+ |
|
| 53 |
+ <!-- Main title --> |
|
| 54 |
+ <a class="navbar-brand" href="..">ggtree</a> |
|
| 55 |
+ </div> |
|
| 56 |
+ |
|
| 57 |
+ <!-- Expanded navigation --> |
|
| 58 |
+ <div class="navbar-collapse collapse"> |
|
| 59 |
+ <!-- Main navigation --> |
|
| 60 |
+ <ul class="nav navbar-nav"> |
|
| 61 |
+ |
|
| 62 |
+ |
|
| 63 |
+ <li > |
|
| 64 |
+ <a href="..">Home</a> |
|
| 65 |
+ </li> |
|
| 66 |
+ |
|
| 67 |
+ |
|
| 68 |
+ |
|
| 69 |
+ <li > |
|
| 70 |
+ <a href="../documentation/">Documentation</a> |
|
| 71 |
+ </li> |
|
| 72 |
+ |
|
| 73 |
+ |
|
| 74 |
+ |
|
| 75 |
+ <li > |
|
| 76 |
+ <a href="../faq/">FAQ</a> |
|
| 77 |
+ </li> |
|
| 78 |
+ |
|
| 79 |
+ |
|
| 80 |
+ |
|
| 81 |
+ <li > |
|
| 82 |
+ <a href="../featuredArticles/">Featured Articles</a> |
|
| 83 |
+ </li> |
|
| 84 |
+ |
|
| 85 |
+ |
|
| 86 |
+ |
|
| 87 |
+ <li class="dropdown active"> |
|
| 88 |
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a> |
|
| 89 |
+ <ul class="dropdown-menu"> |
|
| 90 |
+ |
|
| 91 |
+ |
|
| 92 |
+<li > |
|
| 93 |
+ <a href="../ChIPseeker/">ChIPseeker</a> |
|
| 94 |
+</li> |
|
| 95 |
+ |
|
| 96 |
+ |
|
| 97 |
+ |
|
| 98 |
+<li > |
|
| 99 |
+ <a href="../clusterProfiler/">clusterProfiler</a> |
|
| 100 |
+</li> |
|
| 101 |
+ |
|
| 102 |
+ |
|
| 103 |
+ |
|
| 104 |
+<li class="active"> |
|
| 105 |
+ <a href="./">DOSE</a> |
|
| 106 |
+</li> |
|
| 107 |
+ |
|
| 108 |
+ |
|
| 109 |
+ |
|
| 110 |
+<li > |
|
| 111 |
+ <a href="../ggtree/">ggtree</a> |
|
| 112 |
+</li> |
|
| 113 |
+ |
|
| 114 |
+ |
|
| 115 |
+ |
|
| 116 |
+<li > |
|
| 117 |
+ <a href="../GOSemSim/">GOSemSim</a> |
|
| 118 |
+</li> |
|
| 119 |
+ |
|
| 120 |
+ |
|
| 121 |
+ |
|
| 122 |
+<li > |
|
| 123 |
+ <a href="../ReactomePA/">ReactomePA</a> |
|
| 124 |
+</li> |
|
| 125 |
+ |
|
| 126 |
+ |
|
| 127 |
+ </ul> |
|
| 128 |
+ </li> |
|
| 129 |
+ |
|
| 130 |
+ |
|
| 131 |
+ </ul> |
|
| 132 |
+ |
|
| 133 |
+ <!-- Search, Navigation and Repo links --> |
|
| 134 |
+ <ul class="nav navbar-nav navbar-right"> |
|
| 135 |
+ <li> |
|
| 136 |
+ <a href="#" data-toggle="modal" data-target="#mkdocs_search_modal"> |
|
| 137 |
+ <i class="fa fa-search"></i> Search |
|
| 138 |
+ </a> |
|
| 139 |
+ </li> |
|
| 140 |
+ <li > |
|
| 141 |
+ <a rel="next" href="../clusterProfiler/"> |
|
| 142 |
+ <i class="fa fa-arrow-left"></i> Previous |
|
| 143 |
+ </a> |
|
| 144 |
+ </li> |
|
| 145 |
+ <li > |
|
| 146 |
+ <a rel="prev" href="../ggtree/"> |
|
| 147 |
+ Next <i class="fa fa-arrow-right"></i> |
|
| 148 |
+ </a> |
|
| 149 |
+ </li> |
|
| 150 |
+ |
|
| 151 |
+ <li> |
|
| 152 |
+ <a href="https://github.com/GuangchuangYu/ggtree"> |
|
| 153 |
+ |
|
| 154 |
+ <i class="fa fa-github"></i> |
|
| 155 |
+ |
|
| 156 |
+ GitHub |
|
| 157 |
+ </a> |
|
| 158 |
+ </li> |
|
| 159 |
+ |
|
| 160 |
+ </ul> |
|
| 161 |
+ </div> |
|
| 162 |
+ </div> |
|
| 163 |
+</div> |
|
| 164 |
+ |
|
| 165 |
+ <div class="container"> |
|
| 166 |
+ <div class="col-md-3"><div class="bs-sidebar hidden-print affix well" role="complementary"> |
|
| 167 |
+ <ul class="nav bs-sidenav"> |
|
| 168 |
+ |
|
| 169 |
+ </ul> |
|
| 170 |
+</div></div> |
|
| 171 |
+ <div class="col-md-9" role="main"> |
|
| 172 |
+ |
|
| 173 |
+<p><meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/DOSE" /></p></div> |
|
| 174 |
+ </div> |
|
| 175 |
+ |
|
| 176 |
+ <footer class="col-md-12"> |
|
| 177 |
+ <hr> |
|
| 178 |
+ |
|
| 179 |
+ <center>Copyright © 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&m=0&c=ff0000&cr1=ffffff&sx=0" async="async"></script></div></center> |
|
| 180 |
+ |
|
| 181 |
+ <center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center> |
|
| 182 |
+ </footer> |
|
| 183 |
+ |
|
| 184 |
+ <script src="../js/jquery-1.10.2.min.js"></script> |
|
| 185 |
+ <script src="../js/bootstrap-3.0.3.min.js"></script> |
|
| 186 |
+ <script src="../js/highlight.pack.js"></script> |
|
| 187 |
+ <script>var base_url = '..';</script> |
|
| 188 |
+ <script data-main="../mkdocs/js/search.js" src="../mkdocs/js/require.js"></script> |
|
| 189 |
+ <script src="../js/base.js"></script> |
|
| 190 |
+ |
|
| 191 |
+ <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true"> |
|
| 192 |
+ <div class="modal-dialog"> |
|
| 193 |
+ <div class="modal-content"> |
|
| 194 |
+ <div class="modal-header"> |
|
| 195 |
+ <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">×</span><span class="sr-only">Close</span></button> |
|
| 196 |
+ <h4 class="modal-title" id="exampleModalLabel">Search</h4> |
|
| 197 |
+ </div> |
|
| 198 |
+ <div class="modal-body"> |
|
| 199 |
+ <p> |
|
| 200 |
+ From here you can search these documents. Enter |
|
| 201 |
+ your search terms below. |
|
| 202 |
+ </p> |
|
| 203 |
+ <form role="form"> |
|
| 204 |
+ <div class="form-group"> |
|
| 205 |
+ <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query"> |
|
| 206 |
+ </div> |
|
| 207 |
+ </form> |
|
| 208 |
+ <div id="mkdocs-search-results"></div> |
|
| 209 |
+ </div> |
|
| 210 |
+ <div class="modal-footer"> |
|
| 211 |
+ </div> |
|
| 212 |
+ </div> |
|
| 213 |
+ </div> |
|
| 214 |
+ </div> |
|
| 215 |
+ </body> |
|
| 216 |
+</html> |
|
| 0 | 217 |
\ No newline at end of file |
| 1 | 218 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,216 @@ |
| 1 |
+<!DOCTYPE html> |
|
| 2 |
+<html lang="en"> |
|
| 3 |
+ <head> |
|
| 4 |
+ <meta charset="utf-8"> |
|
| 5 |
+ <meta http-equiv="X-UA-Compatible" content="IE=edge"> |
|
| 6 |
+ <meta name="viewport" content="width=device-width, initial-scale=1.0"> |
|
| 7 |
+ |
|
| 8 |
+ <meta name="author" content="Guangchuang Yu"> |
|
| 9 |
+ <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/GOSemSim/"> |
|
| 10 |
+ <link rel="shortcut icon" href="../img/favicon.ico"> |
|
| 11 |
+ |
|
| 12 |
+ <title>GOSemSim - ggtree</title> |
|
| 13 |
+ |
|
| 14 |
+ <link href="../css/bootstrap-custom.min.css" rel="stylesheet"> |
|
| 15 |
+ <link href="../css/font-awesome-4.0.3.css" rel="stylesheet"> |
|
| 16 |
+ <link rel="stylesheet" href="../css/highlight.css"> |
|
| 17 |
+ <link href="../css/base.css" rel="stylesheet"> |
|
| 18 |
+ |
|
| 19 |
+ <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries --> |
|
| 20 |
+ <!--[if lt IE 9]> |
|
| 21 |
+ <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script> |
|
| 22 |
+ <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script> |
|
| 23 |
+ <![endif]--> |
|
| 24 |
+ |
|
| 25 |
+ |
|
| 26 |
+ <script> |
|
| 27 |
+ (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
|
|
| 28 |
+ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), |
|
| 29 |
+ m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) |
|
| 30 |
+ })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); |
|
| 31 |
+ |
|
| 32 |
+ ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');
|
|
| 33 |
+ ga('send', 'pageview');
|
|
| 34 |
+ </script> |
|
| 35 |
+ |
|
| 36 |
+ </head> |
|
| 37 |
+ |
|
| 38 |
+ <body> |
|
| 39 |
+ |
|
| 40 |
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> |
|
| 41 |
+ <div class="container"> |
|
| 42 |
+ |
|
| 43 |
+ <!-- Collapsed navigation --> |
|
| 44 |
+ <div class="navbar-header"> |
|
| 45 |
+ <!-- Expander button --> |
|
| 46 |
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse"> |
|
| 47 |
+ <span class="sr-only">Toggle navigation</span> |
|
| 48 |
+ <span class="icon-bar"></span> |
|
| 49 |
+ <span class="icon-bar"></span> |
|
| 50 |
+ <span class="icon-bar"></span> |
|
| 51 |
+ </button> |
|
| 52 |
+ |
|
| 53 |
+ <!-- Main title --> |
|
| 54 |
+ <a class="navbar-brand" href="..">ggtree</a> |
|
| 55 |
+ </div> |
|
| 56 |
+ |
|
| 57 |
+ <!-- Expanded navigation --> |
|
| 58 |
+ <div class="navbar-collapse collapse"> |
|
| 59 |
+ <!-- Main navigation --> |
|
| 60 |
+ <ul class="nav navbar-nav"> |
|
| 61 |
+ |
|
| 62 |
+ |
|
| 63 |
+ <li > |
|
| 64 |
+ <a href="..">Home</a> |
|
| 65 |
+ </li> |
|
| 66 |
+ |
|
| 67 |
+ |
|
| 68 |
+ |
|
| 69 |
+ <li > |
|
| 70 |
+ <a href="../documentation/">Documentation</a> |
|
| 71 |
+ </li> |
|
| 72 |
+ |
|
| 73 |
+ |
|
| 74 |
+ |
|
| 75 |
+ <li > |
|
| 76 |
+ <a href="../faq/">FAQ</a> |
|
| 77 |
+ </li> |
|
| 78 |
+ |
|
| 79 |
+ |
|
| 80 |
+ |
|
| 81 |
+ <li > |
|
| 82 |
+ <a href="../featuredArticles/">Featured Articles</a> |
|
| 83 |
+ </li> |
|
| 84 |
+ |
|
| 85 |
+ |
|
| 86 |
+ |
|
| 87 |
+ <li class="dropdown active"> |
|
| 88 |
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a> |
|
| 89 |
+ <ul class="dropdown-menu"> |
|
| 90 |
+ |
|
| 91 |
+ |
|
| 92 |
+<li > |
|
| 93 |
+ <a href="../ChIPseeker/">ChIPseeker</a> |
|
| 94 |
+</li> |
|
| 95 |
+ |
|
| 96 |
+ |
|
| 97 |
+ |
|
| 98 |
+<li > |
|
| 99 |
+ <a href="../clusterProfiler/">clusterProfiler</a> |
|
| 100 |
+</li> |
|
| 101 |
+ |
|
| 102 |
+ |
|
| 103 |
+ |
|
| 104 |
+<li > |
|
| 105 |
+ <a href="../DOSE/">DOSE</a> |
|
| 106 |
+</li> |
|
| 107 |
+ |
|
| 108 |
+ |
|
| 109 |
+ |
|
| 110 |
+<li > |
|
| 111 |
+ <a href="../ggtree/">ggtree</a> |
|
| 112 |
+</li> |
|
| 113 |
+ |
|
| 114 |
+ |
|
| 115 |
+ |
|
| 116 |
+<li class="active"> |
|
| 117 |
+ <a href="./">GOSemSim</a> |
|
| 118 |
+</li> |
|
| 119 |
+ |
|
| 120 |
+ |
|
| 121 |
+ |
|
| 122 |
+<li > |
|
| 123 |
+ <a href="../ReactomePA/">ReactomePA</a> |
|
| 124 |
+</li> |
|
| 125 |
+ |
|
| 126 |
+ |
|
| 127 |
+ </ul> |
|
| 128 |
+ </li> |
|
| 129 |
+ |
|
| 130 |
+ |
|
| 131 |
+ </ul> |
|
| 132 |
+ |
|
| 133 |
+ <!-- Search, Navigation and Repo links --> |
|
| 134 |
+ <ul class="nav navbar-nav navbar-right"> |
|
| 135 |
+ <li> |
|
| 136 |
+ <a href="#" data-toggle="modal" data-target="#mkdocs_search_modal"> |
|
| 137 |
+ <i class="fa fa-search"></i> Search |
|
| 138 |
+ </a> |
|
| 139 |
+ </li> |
|
| 140 |
+ <li > |
|
| 141 |
+ <a rel="next" href="../ggtree/"> |
|
| 142 |
+ <i class="fa fa-arrow-left"></i> Previous |
|
| 143 |
+ </a> |
|
| 144 |
+ </li> |
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| 145 |
+ <li > |
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| 146 |
+ <a rel="prev" href="../ReactomePA/"> |
|
| 147 |
+ Next <i class="fa fa-arrow-right"></i> |
|
| 148 |
+ </a> |
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| 149 |
+ </li> |
|
| 150 |
+ |
|
| 151 |
+ <li> |
|
| 152 |
+ <a href="https://github.com/GuangchuangYu/ggtree"> |
|
| 153 |
+ |
|
| 154 |
+ <i class="fa fa-github"></i> |
|
| 155 |
+ |
|
| 156 |
+ GitHub |
|
| 157 |
+ </a> |
|
| 158 |
+ </li> |
|
| 159 |
+ |
|
| 160 |
+ </ul> |
|
| 161 |
+ </div> |
|
| 162 |
+ </div> |
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| 163 |
+</div> |
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| 164 |
+ |
|
| 165 |
+ <div class="container"> |
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+ <div class="col-md-3"><div class="bs-sidebar hidden-print affix well" role="complementary"> |
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| 167 |
+ <ul class="nav bs-sidenav"> |
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| 168 |
+ |
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| 169 |
+ </ul> |
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| 170 |
+</div></div> |
|
| 171 |
+ <div class="col-md-9" role="main"> |
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| 172 |
+ |
|
| 173 |
+<p><meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/GOSemSim" /></p></div> |
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| 174 |
+ </div> |
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| 175 |
+ |
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| 176 |
+ <footer class="col-md-12"> |
|
| 177 |
+ <hr> |
|
| 178 |
+ |
|
| 179 |
+ <center>Copyright © 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&m=0&c=ff0000&cr1=ffffff&sx=0" async="async"></script></div></center> |
|
| 180 |
+ |
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| 181 |
+ <center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center> |
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| 182 |
+ </footer> |
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+ |
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+ <script src="../js/jquery-1.10.2.min.js"></script> |
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+ <script src="../js/bootstrap-3.0.3.min.js"></script> |
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+ <script src="../js/highlight.pack.js"></script> |
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+ <script>var base_url = '..';</script> |
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+ <script data-main="../mkdocs/js/search.js" src="../mkdocs/js/require.js"></script> |
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| 189 |
+ <script src="../js/base.js"></script> |
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| 190 |
+ |
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| 191 |
+ <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true"> |
|
| 192 |
+ <div class="modal-dialog"> |
|
| 193 |
+ <div class="modal-content"> |
|
| 194 |
+ <div class="modal-header"> |
|
| 195 |
+ <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">×</span><span class="sr-only">Close</span></button> |
|
| 196 |
+ <h4 class="modal-title" id="exampleModalLabel">Search</h4> |
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| 197 |
+ </div> |
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+ <div class="modal-body"> |
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+ <p> |
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| 200 |
+ From here you can search these documents. Enter |
|
| 201 |
+ your search terms below. |
|
| 202 |
+ </p> |
|
| 203 |
+ <form role="form"> |
|
| 204 |
+ <div class="form-group"> |
|
| 205 |
+ <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query"> |
|
| 206 |
+ </div> |
|
| 207 |
+ </form> |
|
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+ <div id="mkdocs-search-results"></div> |
|
| 209 |
+ </div> |
|
| 210 |
+ <div class="modal-footer"> |
|
| 211 |
+ </div> |
|
| 212 |
+ </div> |
|
| 213 |
+ </div> |
|
| 214 |
+ </div> |
|
| 215 |
+ </body> |
|
| 216 |
+</html> |
|
| 0 | 217 |
\ No newline at end of file |
| 1 | 218 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,216 @@ |
| 1 |
+<!DOCTYPE html> |
|
| 2 |
+<html lang="en"> |
|
| 3 |
+ <head> |
|
| 4 |
+ <meta charset="utf-8"> |
|
| 5 |
+ <meta http-equiv="X-UA-Compatible" content="IE=edge"> |
|
| 6 |
+ <meta name="viewport" content="width=device-width, initial-scale=1.0"> |
|
| 7 |
+ |
|
| 8 |
+ <meta name="author" content="Guangchuang Yu"> |
|
| 9 |
+ <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/ReactomePA/"> |
|
| 10 |
+ <link rel="shortcut icon" href="../img/favicon.ico"> |
|
| 11 |
+ |
|
| 12 |
+ <title>ReactomePA - ggtree</title> |
|
| 13 |
+ |
|
| 14 |
+ <link href="../css/bootstrap-custom.min.css" rel="stylesheet"> |
|
| 15 |
+ <link href="../css/font-awesome-4.0.3.css" rel="stylesheet"> |
|
| 16 |
+ <link rel="stylesheet" href="../css/highlight.css"> |
|
| 17 |
+ <link href="../css/base.css" rel="stylesheet"> |
|
| 18 |
+ |
|
| 19 |
+ <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries --> |
|
| 20 |
+ <!--[if lt IE 9]> |
|
| 21 |
+ <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script> |
|
| 22 |
+ <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script> |
|
| 23 |
+ <![endif]--> |
|
| 24 |
+ |
|
| 25 |
+ |
|
| 26 |
+ <script> |
|
| 27 |
+ (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
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|
| 28 |
+ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), |
|
| 29 |
+ m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) |
|
| 30 |
+ })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); |
|
| 31 |
+ |
|
| 32 |
+ ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');
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|
| 33 |
+ ga('send', 'pageview');
|
|
| 34 |
+ </script> |
|
| 35 |
+ |
|
| 36 |
+ </head> |
|
| 37 |
+ |
|
| 38 |
+ <body> |
|
| 39 |
+ |
|
| 40 |
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> |
|
| 41 |
+ <div class="container"> |
|
| 42 |
+ |
|
| 43 |
+ <!-- Collapsed navigation --> |
|
| 44 |
+ <div class="navbar-header"> |
|
| 45 |
+ <!-- Expander button --> |
|
| 46 |
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse"> |
|
| 47 |
+ <span class="sr-only">Toggle navigation</span> |
|
| 48 |
+ <span class="icon-bar"></span> |
|
| 49 |
+ <span class="icon-bar"></span> |
|
| 50 |
+ <span class="icon-bar"></span> |
|
| 51 |
+ </button> |
|
| 52 |
+ |
|
| 53 |
+ <!-- Main title --> |
|
| 54 |
+ <a class="navbar-brand" href="..">ggtree</a> |
|
| 55 |
+ </div> |
|
| 56 |
+ |
|
| 57 |
+ <!-- Expanded navigation --> |
|
| 58 |
+ <div class="navbar-collapse collapse"> |
|
| 59 |
+ <!-- Main navigation --> |
|
| 60 |
+ <ul class="nav navbar-nav"> |
|
| 61 |
+ |
|
| 62 |
+ |
|
| 63 |
+ <li > |
|
| 64 |
+ <a href="..">Home</a> |
|
| 65 |
+ </li> |
|
| 66 |
+ |
|
| 67 |
+ |
|
| 68 |
+ |
|
| 69 |
+ <li > |
|
| 70 |
+ <a href="../documentation/">Documentation</a> |
|
| 71 |
+ </li> |
|
| 72 |
+ |
|
| 73 |
+ |
|
| 74 |
+ |
|
| 75 |
+ <li > |
|
| 76 |
+ <a href="../faq/">FAQ</a> |
|
| 77 |
+ </li> |
|
| 78 |
+ |
|
| 79 |
+ |
|
| 80 |
+ |
|
| 81 |
+ <li > |
|
| 82 |
+ <a href="../featuredArticles/">Featured Articles</a> |
|
| 83 |
+ </li> |
|
| 84 |
+ |
|
| 85 |
+ |
|
| 86 |
+ |
|
| 87 |
+ <li class="dropdown active"> |
|
| 88 |
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a> |
|
| 89 |
+ <ul class="dropdown-menu"> |
|
| 90 |
+ |
|
| 91 |
+ |
|
| 92 |
+<li > |
|
| 93 |
+ <a href="../ChIPseeker/">ChIPseeker</a> |
|
| 94 |
+</li> |
|
| 95 |
+ |
|
| 96 |
+ |
|
| 97 |
+ |
|
| 98 |
+<li > |
|
| 99 |
+ <a href="../clusterProfiler/">clusterProfiler</a> |
|
| 100 |
+</li> |
|
| 101 |
+ |
|
| 102 |
+ |
|
| 103 |
+ |
|
| 104 |
+<li > |
|
| 105 |
+ <a href="../DOSE/">DOSE</a> |
|
| 106 |
+</li> |
|
| 107 |
+ |
|
| 108 |
+ |
|
| 109 |
+ |
|
| 110 |
+<li > |
|
| 111 |
+ <a href="../ggtree/">ggtree</a> |
|
| 112 |
+</li> |
|
| 113 |
+ |
|
| 114 |
+ |
|
| 115 |
+ |
|
| 116 |
+<li > |
|
| 117 |
+ <a href="../GOSemSim/">GOSemSim</a> |
|
| 118 |
+</li> |
|
| 119 |
+ |
|
| 120 |
+ |
|
| 121 |
+ |
|
| 122 |
+<li class="active"> |
|
| 123 |
+ <a href="./">ReactomePA</a> |
|
| 124 |
+</li> |
|
| 125 |
+ |
|
| 126 |
+ |
|
| 127 |
+ </ul> |
|
| 128 |
+ </li> |
|
| 129 |
+ |
|
| 130 |
+ |
|
| 131 |
+ </ul> |
|
| 132 |
+ |
|
| 133 |
+ <!-- Search, Navigation and Repo links --> |
|
| 134 |
+ <ul class="nav navbar-nav navbar-right"> |
|
| 135 |
+ <li> |
|
| 136 |
+ <a href="#" data-toggle="modal" data-target="#mkdocs_search_modal"> |
|
| 137 |
+ <i class="fa fa-search"></i> Search |
|
| 138 |
+ </a> |
|
| 139 |
+ </li> |
|
| 140 |
+ <li > |
|
| 141 |
+ <a rel="next" href="../GOSemSim/"> |
|
| 142 |
+ <i class="fa fa-arrow-left"></i> Previous |
|
| 143 |
+ </a> |
|
| 144 |
+ </li> |
|
| 145 |
+ <li class="disabled"> |
|
| 146 |
+ <a rel="prev" > |
|
| 147 |
+ Next <i class="fa fa-arrow-right"></i> |
|
| 148 |
+ </a> |
|
| 149 |
+ </li> |
|
| 150 |
+ |
|
| 151 |
+ <li> |
|
| 152 |
+ <a href="https://github.com/GuangchuangYu/ggtree"> |
|
| 153 |
+ |
|
| 154 |
+ <i class="fa fa-github"></i> |
|
| 155 |
+ |
|
| 156 |
+ GitHub |
|
| 157 |
+ </a> |
|
| 158 |
+ </li> |
|
| 159 |
+ |
|
| 160 |
+ </ul> |
|
| 161 |
+ </div> |
|
| 162 |
+ </div> |
|
| 163 |
+</div> |
|
| 164 |
+ |
|
| 165 |
+ <div class="container"> |
|
| 166 |
+ <div class="col-md-3"><div class="bs-sidebar hidden-print affix well" role="complementary"> |
|
| 167 |
+ <ul class="nav bs-sidenav"> |
|
| 168 |
+ |
|
| 169 |
+ </ul> |
|
| 170 |
+</div></div> |
|
| 171 |
+ <div class="col-md-9" role="main"> |
|
| 172 |
+ |
|
| 173 |
+<p><meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/ReactomePA" /></p></div> |
|
| 174 |
+ </div> |
|
| 175 |
+ |
|
| 176 |
+ <footer class="col-md-12"> |
|
| 177 |
+ <hr> |
|
| 178 |
+ |
|
| 179 |
+ <center>Copyright © 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&m=0&c=ff0000&cr1=ffffff&sx=0" async="async"></script></div></center> |
|
| 180 |
+ |
|
| 181 |
+ <center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center> |
|
| 182 |
+ </footer> |
|
| 183 |
+ |
|
| 184 |
+ <script src="../js/jquery-1.10.2.min.js"></script> |
|
| 185 |
+ <script src="../js/bootstrap-3.0.3.min.js"></script> |
|
| 186 |
+ <script src="../js/highlight.pack.js"></script> |
|
| 187 |
+ <script>var base_url = '..';</script> |
|
| 188 |
+ <script data-main="../mkdocs/js/search.js" src="../mkdocs/js/require.js"></script> |
|
| 189 |
+ <script src="../js/base.js"></script> |
|
| 190 |
+ |
|
| 191 |
+ <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true"> |
|
| 192 |
+ <div class="modal-dialog"> |
|
| 193 |
+ <div class="modal-content"> |
|
| 194 |
+ <div class="modal-header"> |
|
| 195 |
+ <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">×</span><span class="sr-only">Close</span></button> |
|
| 196 |
+ <h4 class="modal-title" id="exampleModalLabel">Search</h4> |
|
| 197 |
+ </div> |
|
| 198 |
+ <div class="modal-body"> |
|
| 199 |
+ <p> |
|
| 200 |
+ From here you can search these documents. Enter |
|
| 201 |
+ your search terms below. |
|
| 202 |
+ </p> |
|
| 203 |
+ <form role="form"> |
|
| 204 |
+ <div class="form-group"> |
|
| 205 |
+ <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query"> |
|
| 206 |
+ </div> |
|
| 207 |
+ </form> |
|
| 208 |
+ <div id="mkdocs-search-results"></div> |
|
| 209 |
+ </div> |
|
| 210 |
+ <div class="modal-footer"> |
|
| 211 |
+ </div> |
|
| 212 |
+ </div> |
|
| 213 |
+ </div> |
|
| 214 |
+ </div> |
|
| 215 |
+ </body> |
|
| 216 |
+</html> |
|
| 0 | 217 |
\ No newline at end of file |
| 1 | 218 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,94 @@ |
| 1 |
+<!DOCTYPE html> |
|
| 2 |
+<html lang="en"> |
|
| 3 |
+ <head> |
|
| 4 |
+ <meta charset="utf-8"> |
|
| 5 |
+ <meta http-equiv="X-UA-Compatible" content="IE=edge"> |
|
| 6 |
+ <meta name="viewport" content="width=device-width, initial-scale=1.0"> |
|
| 7 |
+ {% if page_description %}<meta name="description" content="{{ page_description }}">{% endif %}
|
|
| 8 |
+ {% if site_author %}<meta name="author" content="{{ site_author }}">{% endif %}
|
|
| 9 |
+ {% if canonical_url %}<link rel="canonical" href="{{ canonical_url }}">{% endif %}
|
|
| 10 |
+ {% if favicon %}<link rel="shortcut icon" href="{{ favicon }}">
|
|
| 11 |
+ {% else %}<link rel="shortcut icon" href="{{ base_url }}/img/favicon.ico">{% endif %}
|
|
| 12 |
+ |
|
| 13 |
+ <title>{% if page_title %}{{ page_title }} - {% endif %}{{ site_name }}</title>
|
|
| 14 |
+ |
|
| 15 |
+ <link href="{{ base_url }}/css/bootstrap-custom.min.css" rel="stylesheet">
|
|
| 16 |
+ <link href="{{ base_url }}/css/font-awesome-4.0.3.css" rel="stylesheet">
|
|
| 17 |
+ <link rel="stylesheet" href="{{ base_url }}/css/highlight.css">
|
|
| 18 |
+ <link href="{{ base_url }}/css/base.css" rel="stylesheet">
|
|
| 19 |
+ {%- for path in extra_css %}
|
|
| 20 |
+ <link href="{{ path }}" rel="stylesheet">
|
|
| 21 |
+ {%- endfor %}
|
|
| 22 |
+ |
|
| 23 |
+ <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries --> |
|
| 24 |
+ <!--[if lt IE 9]> |
|
| 25 |
+ <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script> |
|
| 26 |
+ <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script> |
|
| 27 |
+ <![endif]--> |
|
| 28 |
+ |
|
| 29 |
+ {% if google_analytics %}
|
|
| 30 |
+ <script> |
|
| 31 |
+ (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
|
|
| 32 |
+ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), |
|
| 33 |
+ m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) |
|
| 34 |
+ })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); |
|
| 35 |
+ |
|
| 36 |
+ ga('create', '{{ google_analytics[0] }}', '{{ google_analytics[1] }}');
|
|
| 37 |
+ ga('send', 'pageview');
|
|
| 38 |
+ </script> |
|
| 39 |
+ {% endif %}
|
|
| 40 |
+ </head> |
|
| 41 |
+ |
|
| 42 |
+ <body> |
|
| 43 |
+ |
|
| 44 |
+ {% include "nav.html" %}
|
|
| 45 |
+ |
|
| 46 |
+ <div class="container"> |
|
| 47 |
+ <div class="col-md-3">{% include "toc.html" %}</div>
|
|
| 48 |
+ <div class="col-md-9" role="main">{% include "content.html" %}</div>
|
|
| 49 |
+ </div> |
|
| 50 |
+ |
|
| 51 |
+ <footer class="col-md-12"> |
|
| 52 |
+ <hr> |
|
| 53 |
+ {% if copyright %}
|
|
| 54 |
+ <center>{{ copyright }}</center>
|
|
| 55 |
+ {% endif %}
|
|
| 56 |
+ <center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center> |
|
| 57 |
+ </footer> |
|
| 58 |
+ |
|
| 59 |
+ <script src="{{ base_url }}/js/jquery-1.10.2.min.js"></script>
|
|
| 60 |
+ <script src="{{ base_url }}/js/bootstrap-3.0.3.min.js"></script>
|
|
| 61 |
+ <script src="{{ base_url }}/js/highlight.pack.js"></script>
|
|
| 62 |
+ <script>var base_url = '{{ base_url }}';</script>
|
|
| 63 |
+ <script data-main="{{ base_url }}/mkdocs/js/search.js" src="{{ base_url }}/mkdocs/js/require.js"></script>
|
|
| 64 |
+ <script src="{{ base_url }}/js/base.js"></script>
|
|
| 65 |
+ {%- for path in extra_javascript %}
|
|
| 66 |
+ <script src="{{ path }}"></script>
|
|
| 67 |
+ {%- endfor %}
|
|
| 68 |
+ |
|
| 69 |
+ <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true"> |
|
| 70 |
+ <div class="modal-dialog"> |
|
| 71 |
+ <div class="modal-content"> |
|
| 72 |
+ <div class="modal-header"> |
|
| 73 |
+ <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">×</span><span class="sr-only">Close</span></button> |
|
| 74 |
+ <h4 class="modal-title" id="exampleModalLabel">Search</h4> |
|
| 75 |
+ </div> |
|
| 76 |
+ <div class="modal-body"> |
|
| 77 |
+ <p> |
|
| 78 |
+ From here you can search these documents. Enter |
|
| 79 |
+ your search terms below. |
|
| 80 |
+ </p> |
|
| 81 |
+ <form role="form"> |
|
| 82 |
+ <div class="form-group"> |
|
| 83 |
+ <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query"> |
|
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+ </div> |
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+ </form> |
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+ <div id="mkdocs-search-results"></div> |
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+ </div> |
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+ <div class="modal-footer"> |
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+ </div> |
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+ </div> |
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+ </div> |
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+ </div> |
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+ </body> |
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+</html> |
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+<!DOCTYPE html> |
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+<html lang="en"> |
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+ <head> |
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+ <meta charset="utf-8"> |
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+ <meta http-equiv="X-UA-Compatible" content="IE=edge"> |
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0"> |
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+ |
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+ <meta name="author" content="Guangchuang Yu"> |
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+ <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/clusterProfiler/"> |
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+ <link rel="shortcut icon" href="../img/favicon.ico"> |
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+ |
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+ <title>clusterProfiler - ggtree</title> |
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+ |
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+ <link href="../css/bootstrap-custom.min.css" rel="stylesheet"> |
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+ <link href="../css/font-awesome-4.0.3.css" rel="stylesheet"> |
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+ <link rel="stylesheet" href="../css/highlight.css"> |
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+ <link href="../css/base.css" rel="stylesheet"> |
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+ |
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+ <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries --> |
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+ <!--[if lt IE 9]> |
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+ <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script> |
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+ <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script> |
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+ <![endif]--> |
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+ |
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+ |
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+ <script> |
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+ (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
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+ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), |
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+ m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) |
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+ })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); |
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+ |
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+ ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');
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+ ga('send', 'pageview');
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+ </script> |
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+ |
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+ </head> |
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+ |
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+ <body> |
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+ |
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+ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> |
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+ <div class="container"> |
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+ |
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+ <!-- Collapsed navigation --> |
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+ <div class="navbar-header"> |
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+ <!-- Expander button --> |
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+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse"> |
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+ <span class="sr-only">Toggle navigation</span> |
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+ <span class="icon-bar"></span> |
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+ <span class="icon-bar"></span> |
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+ <span class="icon-bar"></span> |
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+ </button> |
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+ |
|
| 53 |
+ <!-- Main title --> |
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| 54 |
+ <a class="navbar-brand" href="..">ggtree</a> |
|
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+ </div> |
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+ |
|
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+ <!-- Expanded navigation --> |
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+ <div class="navbar-collapse collapse"> |
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| 59 |
+ <!-- Main navigation --> |
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+ <ul class="nav navbar-nav"> |
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+ |
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+ |
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+ <li > |
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+ <a href="..">Home</a> |
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+ </li> |
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+ |
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+ |
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+ |
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+ <li > |
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+ <a href="../documentation/">Documentation</a> |
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+ </li> |
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+ |
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+ |
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+ |
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+ <li > |
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+ <a href="../faq/">FAQ</a> |
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+ </li> |
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+ |
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+ |
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+ |
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+ <li > |
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+ <a href="../featuredArticles/">Featured Articles</a> |
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+ </li> |
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+ |
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+ |
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+ |
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+ <li class="dropdown active"> |
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+ <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a> |
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+ <ul class="dropdown-menu"> |
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+ |
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+ |
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+<li > |
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+ <a href="../ChIPseeker/">ChIPseeker</a> |
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+</li> |
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+ |
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+ |
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+ |
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+<li class="active"> |
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+ <a href="./">clusterProfiler</a> |
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+</li> |
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+ |
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+ |
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+ |
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+<li > |
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+ <a href="../DOSE/">DOSE</a> |
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+</li> |
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+ |
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+ |
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+ |
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+<li > |
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+ <a href="../ggtree/">ggtree</a> |
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+</li> |
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+ |
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+ |
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+ |
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+<li > |
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+ <a href="../GOSemSim/">GOSemSim</a> |
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+</li> |
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+ |
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| 120 |
+ |
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| 121 |
+ |
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+<li > |
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+ <a href="../ReactomePA/">ReactomePA</a> |
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+</li> |
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+ |
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| 126 |
+ |
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+ </ul> |
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+ </li> |
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+ |
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+ |
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+ </ul> |
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| 132 |
+ |
|
| 133 |
+ <!-- Search, Navigation and Repo links --> |
|
| 134 |
+ <ul class="nav navbar-nav navbar-right"> |
|
| 135 |
+ <li> |
|
| 136 |
+ <a href="#" data-toggle="modal" data-target="#mkdocs_search_modal"> |
|
| 137 |
+ <i class="fa fa-search"></i> Search |
|
| 138 |
+ </a> |
|
| 139 |
+ </li> |
|
| 140 |
+ <li > |
|
| 141 |
+ <a rel="next" href="../ChIPseeker/"> |
|
| 142 |
+ <i class="fa fa-arrow-left"></i> Previous |
|
| 143 |
+ </a> |
|
| 144 |
+ </li> |
|
| 145 |
+ <li > |
|
| 146 |
+ <a rel="prev" href="../DOSE/"> |
|
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+ Next <i class="fa fa-arrow-right"></i> |
|
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+ </a> |
|
| 149 |
+ </li> |
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| 150 |
+ |
|
| 151 |
+ <li> |
|
| 152 |
+ <a href="https://github.com/GuangchuangYu/ggtree"> |
|
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+ |
|
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+ <i class="fa fa-github"></i> |
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+ |
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+ GitHub |
|
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+ </a> |
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+ </li> |
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+ |
|