update docs

DESCRIPTION

@@ -30,7 +30,7 @@ Imports:
     stats,
     utils
 Suggests:
-    BiocStyle,
+    prettydoc,
     clusterProfiler,
     knitr,
     org.Hs.eg.db,
@@ -43,4 +43,4 @@ BugReports: https://github.com/GuangchuangYu/DOSE/issues
 Packaged: 2011-12-28 08:16:14 UTC; root
 biocViews: Annotation, Visualization, MultipleComparison, GeneSetEnrichment,
     Pathways, Software
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0

README.Rmd

@@ -1,7 +1,7 @@
 ---
 output:
   md_document:
-    variant: markdown_github
+    variant: gfm
 html_preview: false
 ---
 

README.md

@@ -1,38 +1,65 @@
-DOSE: Disease Ontology Semantic and Enrichment analysis
-=======================================================
-
-[![](https://img.shields.io/badge/release%20version-3.4.0-green.svg)](https://bioconductor.org/packages/DOSE) [![](https://img.shields.io/badge/devel%20version-3.5.1-green.svg)](https://github.com/guangchuangyu/DOSE) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/DOSE.svg)](https://www.bioconductor.org/packages/devel/bioc/html/DOSE.html#since)
-
-[![platform](http://www.bioconductor.org/shields/availability/devel/DOSE.svg)](https://www.bioconductor.org/packages/devel/bioc/html/DOSE.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/DOSE.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/DOSE/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/DOSE/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/DOSE) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/DOSE/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/DOSE)
-
-[![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/DOSE/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/DOSE/) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--04--09-green.svg)](https://github.com/GuangchuangYu/DOSE/commits/master)
-
-This package implements five methods proposed by *Resnik*, *Schlicker*, *Jiang*, *Lin* and *Wang* respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.
-
-For details, please visit our project website, <https://guangchuangyu.github.io/software/DOSE>.
-
--   [Documentation](https://guangchuangyu.github.io/software/DOSE/documentation/)
--   [Featured Articles](https://guangchuangyu.github.io/software/DOSE/featuredArticles/)
--   [Feedback](https://guangchuangyu.github.io/software/DOSE/#feedback)
-
-[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=DOSE&url=http://bioinformatics.oxfordjournals.org/content/31/4/608) [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu) [![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg)](https://guangchuangyu.github.io/blog_images/biobabble.jpg) [![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
-
-------------------------------------------------------------------------
+# DOSE: Disease Ontology Semantic and Enrichment analysis
+
+[![releaseVersion](https://img.shields.io/badge/release%20version-3.6.1-green.svg?style=flat)](https://bioconductor.org/packages/DOSE)
+[![develVersion](https://img.shields.io/badge/devel%20version-3.7.1-green.svg?style=flat)](https://github.com/guangchuangyu/DOSE)
+[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/DOSE.svg)](https://www.bioconductor.org/packages/devel/bioc/html/DOSE.html#since)
+
+[![platform](http://www.bioconductor.org/shields/availability/devel/DOSE.svg)](https://www.bioconductor.org/packages/devel/bioc/html/DOSE.html#archives)
+[![Build
+Status](http://www.bioconductor.org/shields/build/devel/bioc/DOSE.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/DOSE/)
+[![Linux/Mac Travis Build
+Status](https://img.shields.io/travis/GuangchuangYu/DOSE/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/DOSE)
+[![AppVeyor Build
+Status](https://img.shields.io/appveyor/ci/Guangchuangyu/DOSE/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/DOSE)
+
+[![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/DOSE/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/DOSE/)
+[![Last-changedate](https://img.shields.io/badge/last%20change-2018--09--30-green.svg)](https://github.com/GuangchuangYu/DOSE/commits/master)
+
+This package implements five methods proposed by *Resnik*, *Schlicker*,
+*Jiang*, *Lin* and *Wang* respectively for measuring semantic
+similarities among DO terms and gene products. Enrichment analyses
+including hypergeometric model and gene set enrichment analysis are also
+implemented for discovering disease associations of high-throughput
+biological data.
+
+For details, please visit our project website,
+<https://guangchuangyu.github.io/software/DOSE>.
+
+  - [Documentation](https://guangchuangyu.github.io/software/DOSE/documentation/)
+  - [Featured
+    Articles](https://guangchuangyu.github.io/software/DOSE/featuredArticles/)
+  - [Feedback](https://guangchuangyu.github.io/software/DOSE/#feedback)
+
+[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=DOSE&url=http://bioinformatics.oxfordjournals.org/content/31/4/608)
+[![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
+[![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/biobabble.jpg)
+[![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
+
+-----
 
 Please cite the following article when using `DOSE`:
 
-***G Yu***, LG Wang, GR Yan, QY He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. ***Bioinformatics*** 2015, 31(4):608-609.
+***G Yu***, LG Wang, GR Yan, QY He. DOSE: an R/Bioconductor package for
+Disease Ontology Semantic and Enrichment analysis. ***Bioinformatics***
+2015,
+31(4):608-609.
 
-[![](https://img.shields.io/badge/doi-10.1093/bioinformatics/btu684-green.svg)](http://dx.doi.org/10.1093/bioinformatics/btu684) [![](https://img.shields.io/badge/Altmetric-26-green.svg)](https://www.altmetric.com/details/2788597)
+[![doi](https://img.shields.io/badge/doi-10.1093/bioinformatics/btu684-green.svg?style=flat)](http://dx.doi.org/10.1093/bioinformatics/btu684)
+[![Altmetric](https://img.shields.io/badge/Altmetric-26-green.svg?style=flat)](https://www.altmetric.com/details/2788597)
 
-------------------------------------------------------------------------
+-----
 
 ### Citation
 
 <img src="https://guangchuangyu.github.io/software/DOSE/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
 
 ### Download stats
 
-[![download](http://www.bioconductor.org/shields/downloads/DOSE.svg)](https://bioconductor.org/packages/stats/bioc/DOSE) [![](https://img.shields.io/badge/download-65637/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/DOSE) [![](https://img.shields.io/badge/download-2907/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/DOSE)
+[![download](http://www.bioconductor.org/shields/downloads/DOSE.svg)](https://bioconductor.org/packages/stats/bioc/DOSE)
+[![total](https://img.shields.io/badge/downloads-85376/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/DOSE)
+[![month](https://img.shields.io/badge/downloads-3396/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/DOSE)
 
 <img src="https://guangchuangyu.github.io/software/DOSE/index_files/figure-html/dlstats-1.png" width="890"/>

vignettes/DOSE.Rmd

@@ -1,17 +1,17 @@
 ---
 title: "Disease Ontology Semantic and Enrichment analysis"
-author: "\\
+author: "Guangchuang Yu\\
 
-	Guangchuang Yu (<[email protected]>)\\
-
-        School of Public Health, The University of Hong Kong"
+        School of Basic Medical Sciences, Southern Medical University"
 date: "`r Sys.Date()`"
 bibliography: DOSE.bib
-csl: nature.csl
+biblio-style: apalike
 output:
-  BiocStyle::html_document:
+  prettydoc::html_pretty:
     toc: true
-  BiocStyle::pdf_document:
+    theme: cayman
+    highlight: github
+  pdf_document:
     toc: true
 vignette: >
   %\VignetteIndexEntry{00 DOSE introduction}
@@ -22,17 +22,27 @@ vignette: >
 ---
 
 ```{r style, echo=FALSE, results="asis", message=FALSE}
-BiocStyle::markdown()
 knitr::opts_chunk$set(tidy = FALSE,
                       warning = FALSE,
                       message = FALSE)
+
+CRANpkg <- function (pkg) {
+    cran <- "https://CRAN.R-project.org/package"
+    fmt <- "[%s](%s=%s)"
+    sprintf(fmt, pkg, cran, pkg)
+}
+
+Biocpkg <- function (pkg) {
+    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)
+}
+
 ```
 
+
 ```{r echo=FALSE, results='hide', message=FALSE}
 library(DOSE)
 ```
 
-
 Disease Ontology (DO)[@schriml_disease_2011] aims to provide an open source ontology for the integration of biomedical data that is associated with human disease.
 We developed `r Biocpkg("DOSE")`[@yu_dose_2015] package to promote the investigation of diseases. `r Biocpkg("DOSE")` provides five methods including _Resnik_, _Lin_, _Jiang_, _Rel_ and _Wang_ for measuring semantic similarities among DO terms and gene products; Hypergeometric model and Gene Set Enrichment Analysis (GSEA) were also implemented for extracting disease association insight from genome wide expression profiles.
 
@@ -72,8 +82,6 @@ to [Bioconductor support site](https://support.bioconductor.org/) and tag your
 post with *DOSE*.
 
 
-For Chinese user, you can follow me on [WeChat (微信)](https://guangchuangyu.github.io/blog_images/biobabble.jpg).
-
 
 # Session Information
 

vignettes/GSEA.Rmd

@@ -1,17 +1,17 @@
 ---
 title: "Disease Gene Set Enrichment Analysis"
-author: "\\
+author: "Guangchuang Yu\\
 
-	Guangchuang Yu (<[email protected]>)\\
-
-        School of Public Health, The University of Hong Kong"
+        School of Basic Medical Sciences, Southern Medical University"
 date: "`r Sys.Date()`"
 bibliography: DOSE.bib
-csl: nature.csl
+biblio-style: apalike
 output:
-  BiocStyle::html_document:
+  prettydoc::html_pretty:
     toc: true
-  BiocStyle::pdf_document:
+    theme: cayman
+    highlight: github
+  pdf_document:
     toc: true
 vignette: >
   %\VignetteIndexEntry{03 Disease GSEA}
@@ -21,10 +21,19 @@ vignette: >
 ---
 
 ```{r style, echo=FALSE, results="asis", message=FALSE}
-BiocStyle::markdown()
 knitr::opts_chunk$set(tidy = FALSE,
                       warning = FALSE,
                       message = FALSE)
+
+CRANpkg <- function (pkg) {
+    cran <- "https://CRAN.R-project.org/package"
+    fmt <- "[%s](%s=%s)"
+    sprintf(fmt, pkg, cran, pkg)
+}
+
+Biocpkg <- function (pkg) {
+    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)
+}
 ```
 
 ```{r echo=FALSE, results='hide', message=FALSE}

vignettes/enrichmentAnalysis.Rmd

@@ -1,17 +1,17 @@
 ---
 title: "Disease enrichment analysis"
-author: "\\
+author: "Guangchuang Yu\\
 
-	Guangchuang Yu (<[email protected]>)\\
-
-        School of Public Health, The University of Hong Kong"
+        School of Basic Medical Sciences, Southern Medical University"
 date: "`r Sys.Date()`"
 bibliography: DOSE.bib
-csl: nature.csl
+biblio-style: apalike
 output:
-  BiocStyle::html_document:
+  prettydoc::html_pretty:
     toc: true
-  BiocStyle::pdf_document:
+    theme: cayman
+    highlight: github
+  pdf_document:
     toc: true
 vignette: >
   %\VignetteIndexEntry{02 Disease enrichment analysis}
@@ -21,10 +21,20 @@ vignette: >
 ---
 
 ```{r style, echo=FALSE, results="asis", message=FALSE}
-BiocStyle::markdown()
 knitr::opts_chunk$set(tidy = FALSE,
                       warning = FALSE,
                       message = FALSE)
+
+CRANpkg <- function (pkg) {
+    cran <- "https://CRAN.R-project.org/package"
+    fmt <- "[%s](%s=%s)"
+    sprintf(fmt, pkg, cran, pkg)
+}
+
+Biocpkg <- function (pkg) {
+    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)
+}
+
 ```
 
 ```{r echo=FALSE, results='hide', message=FALSE}