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YuLab-SMU · Jul 4, 2021 · d0e8b03 · d0e8b03
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: clusterProfiler
 Type: Package
 Title: statistical analysis and visualization of functional profiles for
     genes and gene clusters
-Version: 4.1.0
+Version: 4.1.1
 Authors@R: c(
     person(given = "Guangchuang", family = "Yu",        email = "guangchuangyu@gmail.com",   role  = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),
     person(given = "Li-Gen",      family = "Wang",      email = "reeganwang020@gmail.com",   role  = "ctb"),
@@ -14,7 +14,7 @@ Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
 Description: This package implements methods to analyze and visualize
     functional profiles (GO and KEGG) of gene and gene clusters.
 Depends:
-    R (>= 3.4.0)
+    R (>= 3.5.0)
 Imports:
     AnnotationDbi,
     downloader,

diff --git a/Makefile b/Makefile
@@ -10,7 +10,7 @@ rd:
 	Rscript -e 'library(methods); devtools::document()'
 
 readme:
-	Rscript -e 'rmarkdown::render("README.Rmd", encoding="UTF-8")'
+	Rscript -e 'rmarkdown::render("README.Rmd", rmarkdown::md_document(variant="gfm"), encoding="UTF-8")'
 
 build:
 	cd ..;\

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+# clusterProfiler 4.0.1
+
++ add citation (new paper published on The Innovation) (2021-07-04, Sun)
+
+# clusterProfiler 4.0.0
+
++ Bioconductor 3.13 release
+
+
 # clusterProfiler 3.99.1
 
 + Add new data set, `DE_GSE8057`, which contains DE genes obtained from GSE8057 (2020-03-08, Mon)

diff --git a/R/zzz.R b/R/zzz.R
@@ -2,7 +2,7 @@
 .onAttach <- function(libname, pkgname) {
     pkgVersion <- packageDescription(pkgname, fields="Version")
     msg <- paste0(pkgname, " v", pkgVersion, "  ",
-                  "For help: https://guangchuangyu.github.io/software/", pkgname, "\n\n")
+                  "For help: https://yulab-smu.top/biomedical-knowledge-mining-book/", pkgname, "\n\n")
 
     if (capabilities("libcurl")) {
         dl.method <- "libcurl"
@@ -14,9 +14,11 @@
     options(timeout = max(300, getOption("timeout"))) # see ?download.file
 
     citation <- paste0("If you use ", pkgname, " in published research, please cite:\n",
-                       "Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. ",
-                       "clusterProfiler: an R package for comparing biological themes among gene clusters. ",
-                       "OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.")
+                       "T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, ",
+                       "W Tang, L Zhan, X Fu, S Liu, X Bo*, and G Yu. ", 
+                       "clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. ", 
+                       "The Innovation. 2021, doi: 10.1016/j.xinn.2021.100141")
+
 
     packageStartupMessage(paste0(msg, citation))
 }

diff --git a/README.Rmd b/README.Rmd
@@ -1,14 +1,7 @@
----
-output:
-  md_document:
-    variant: gfm
-html_preview: false
----
-
 
 ```{r echo=FALSE, results="hide", message=FALSE}
 library("badger")
-library("ypages")
+#library("ypages")
 ```
 
 
@@ -46,7 +39,7 @@ Guangchuang YU
 
 School of Basic Medical Sciences, Southern Medical University
 
-<https://guangchuangyu.github.io>
+<https://yulab-smu.top>
 
 
 [![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=clusterProfiler&url=http://online.liebertpub.com/doi/abs/10.1089/omi.2011.0118&screen_name=guangchuangyu)
@@ -58,17 +51,21 @@ School of Basic Medical Sciences, Southern Medical University
 
 Please cite the following article when using `clusterProfiler`:
 
-__*Yu G*__, Wang L, Han Y and He Q^\*^. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
+T Wu<sup>#</sup>, E Hu<sup>#</sup>, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo<sup>\*</sup>, and **G Yu**<sup>\*</sup>. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. **_The Innovation_**. 2021. doi: <https://doi.org/10.1016/j.xinn.2021.100141>
 
 
-`r badge_custom("1st most cited paper", "in OMICS", "green",
-  "http://online.liebertpub.com/action/showMostCitedArticles?journalCode=omi")`
-`r badge_custom("ESI", "Highly Cited Paper", "green")`
-`r badge_doi("10.1089/omi.2011.0118", "green")`
 
 
 <!--
 
+
+
+ r badge_custom("1st most cited paper", "in OMICS", "green",
+  "http://online.liebertpub.com/action/showMostCitedArticles?journalCode=omi")`
+ r badge_custom("ESI", "Highly Cited Paper", "green")`
+ r badge_doi("10.1089/omi.2011.0118", "green")`
+
+
 ------------------------------------------------------------------------
 
 ### Citation

diff --git a/README.md b/README.md
@@ -5,8 +5,8 @@
 [![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)
-[![](https://img.shields.io/badge/release%20version-3.14.0-green.svg)](https://www.bioconductor.org/packages/clusterProfiler)
-[![](https://img.shields.io/badge/devel%20version-3.15.1-green.svg)](https://github.com/guangchuangyu/clusterProfiler)
+[![](https://img.shields.io/badge/release%20version-4.0.0-green.svg)](https://www.bioconductor.org/packages/clusterProfiler)
+[![](https://img.shields.io/badge/devel%20version-4.1.1-green.svg)](https://github.com/guangchuangyu/clusterProfiler)
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/clusterProfiler.svg)](https://www.bioconductor.org/packages/devel/bioc/html/clusterProfiler.html#since)
 
 [![platform](http://www.bioconductor.org/shields/availability/devel/clusterProfiler.svg)](https://www.bioconductor.org/packages/devel/bioc/html/clusterProfiler.html#archives)
@@ -19,7 +19,7 @@ Status](https://img.shields.io/appveyor/ci/Guangchuangyu/clusterProfiler/master.
 [![codecov](https://codecov.io/gh/GuangchuangYu/clusterProfiler/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/clusterProfiler/)
 
 <!--
-[![Last-changedate](https://img.shields.io/badge/last%20change-2019--12--02-green.svg)](https://github.com/GuangchuangYu/clusterProfiler/commits/master)
+[![Last-changedate](https://img.shields.io/badge/last%20change-2021--07--04-green.svg)](https://github.com/GuangchuangYu/clusterProfiler/commits/master)
 -->
 
 This package implements methods to analyze and visualize functional
@@ -28,34 +28,40 @@ profiles of genomic coordinates (supported by
 gene clusters.
 
 For details, please visit
-<https://yulab-smu.github.io/clusterProfiler-book/>.
+<https://yulab-smu.top/biomedical-knowledge-mining-book/>.
 
 ## :writing\_hand: Authors
 
 Guangchuang YU
 
 School of Basic Medical Sciences, Southern Medical University
 
-<https://guangchuangyu.github.io>
+<https://yulab-smu.top>
 
 [![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=clusterProfiler&url=http://online.liebertpub.com/doi/abs/10.1089/omi.2011.0118&screen_name=guangchuangyu)
 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
 [![](https://img.shields.io/badge/follow%20me%20on-WeChat-green.svg)](https://guangchuangyu.github.io/blog_images/biobabble.jpg)
 
------
+------------------------------------------------------------------------
 
 Please cite the following article when using `clusterProfiler`:
 
-***Yu G***, Wang L, Han Y and He Q<sup>\*</sup>. clusterProfiler: an R
-package for comparing biological themes among gene clusters. OMICS: A
-Journal of Integrative Biology. 2012, 16(5):284-287.
-
-[![](https://img.shields.io/badge/1st%20most%20cited%20paper-in%20OMICS-green.svg)](http://online.liebertpub.com/action/showMostCitedArticles?journalCode=omi)
-![](https://img.shields.io/badge/ESI-Highly%20Cited%20Paper-green.svg)
-[![](https://img.shields.io/badge/doi-10.1089/omi.2011.0118-green.svg)](https://doi.org/10.1089/omi.2011.0118)
+T Wu<sup>\#</sup>, E Hu<sup>\#</sup>, S Xu, M Chen, P Guo, Z Dai, T
+Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo<sup>\*</sup>, and **G
+Yu**<sup>\*</sup>. clusterProfiler 4.0: A universal enrichment tool for
+interpreting omics data. ***The Innovation***. 2021. doi:
+<https://doi.org/10.1016/j.xinn.2021.100141>
 
 <!--
 
+
+
+ r badge_custom("1st most cited paper", "in OMICS", "green",
+  "http://online.liebertpub.com/action/showMostCitedArticles?journalCode=omi")`
+ r badge_custom("ESI", "Highly Cited Paper", "green")`
+ r badge_doi("10.1089/omi.2011.0118", "green")`
+
+
 ------------------------------------------------------------------------
 
 ### Citation

diff --git a/inst/CITATION b/inst/CITATION
@@ -1,4 +1,36 @@
-citHeader("Please cite G. Yu (2012) for using clusterProfiler. In addition, please cite G. Yu (2010) when using GOSemSim, G. Yu (2015) when using DOSE and G. Yu (2015) when using ChIPseeker.")
+citHeader("Please cite T. Wu (2021) for using clusterProfiler. In addition, please cite G. Yu (2010) when using GOSemSim, G. Yu (2015) when using DOSE and G. Yu (2015) when using ChIPseeker.")
+
+
+citEntry(entry  ="ARTICLE",
+         title  = "clusterProfiler 4.0: A universal enrichment tool for interpreting omics data",
+         author = personList(
+             as.person("Tianzhi Wu"),
+             as.person("Erqiang Hu"),
+             as.person("Shuangbin Xu"),
+             as.person("Meijun Chen"),
+             as.person("Pingfan Guo"),
+             as.person("Zehan Dai"),
+             as.person("Tingze Feng"),
+             as.person("Lang Zhou"),
+             as.person("Wenli Tang"),
+             as.person("Li Zhan"),
+             as.person("xiaochong Fu"),
+             as.person("Shanshan Liu"),
+             as.person("Xiaochen Bo"),
+             as.person("Guangchuang Yu")
+             ),
+         journal = "The Innovation",
+         year    = "2021",
+         volume  = "2",
+         number  = "3",
+         pages   = "100141",
+         PMID    = "",
+         doi     = "10.1016/j.xinn.2021.100141",
+         textVersion = paste("T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou,",
+                             "W Tang, L Zhan, X Fu, S Liu, X Bo*, and G Yu.", 
+                             "clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.", 
+                             "The Innovation. 2021, doi: 10.1016/j.xinn.2021.100141")
+         )
 
 citEntry(entry  ="ARTICLE",
          title  = "clusterProfiler: an R package for comparing biological themes among gene clusters",