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| Original file line number | Diff line number | Diff line change |
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| .svnignore | ||
| ^.*\.DS_Store | ||
| Makefile | ||
| .travis.yml | ||
| appveyor.yml | ||
| README.Rmd |
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| .git | ||
| Makefile | ||
| README.Rmd | ||
| appveyor.yml | ||
| .travis.yml |
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| ## reference: http://docs.travis-ci.com/user/languages/r/ | ||
|
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| language: r | ||
| r: | ||
| - devel | ||
| - bioc-devel | ||
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| cache: packages | ||
| bioc_required: true | ||
| bioc_use_devel: true | ||
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| os: | ||
| - linux | ||
| - osx | ||
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| env: | ||
| global: | ||
| - _R_CHECK_FORCE_SUGGESTS_=False | ||
| - R_LIBS="http://cran.rstudio.com" | ||
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| r_packages: | ||
| - knitr | ||
| - rmarkdown | ||
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| bioc_packages: | ||
| - DO.db | ||
| - org.Hs.eg.db | ||
| - DOSE | ||
| - reactome.db | ||
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| after_failure: | ||
| - ./travis-tool.sh dump_logs | ||
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| r_github_packages: | ||
| - jimhester/covr | ||
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||
| after_success: | ||
| - Rscript -e 'library(covr); codecov()' | ||
|
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| notifications: | ||
| email: | ||
| recipients: [email protected] | ||
| on_success: never | ||
| on_failure: always | ||
|
|
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| Package: ReactomePA | ||
| Type: Package | ||
| Title: Reactome Pathway Analysis | ||
| Version: 1.17.3 | ||
| Version: 1.17.4 | ||
| Authors@R: c(person(given = "Guangchuang", family = "Yu", | ||
| email = "[email protected]", | ||
| role = c("aut", "cre")), | ||
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@@ -26,7 +26,8 @@ Suggests: | |
| BiocStyle, | ||
| clusterProfiler, | ||
| knitr, | ||
| org.Hs.eg.db | ||
| org.Hs.eg.db, | ||
| testthat | ||
| VignetteBuilder: knitr | ||
| ByteCompile: true | ||
| License: GPL-2 | ||
|
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| --- | ||
| output: | ||
| md_document: | ||
| variant: markdown_github | ||
| html_preview: false | ||
| --- | ||
|
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| # ReactomePA: Reactome Pathway Analysis | ||
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| [](https://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#archives) | ||
| [](https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomePA/) | ||
| [](https://travis-ci.org/GuangchuangYu/ReactomePA) | ||
| [](https://ci.appveyor.com/project/GuangchuangYu/ReactomePA) | ||
| [](http://bioconda.github.io/recipes/bioconductor-reactomepa/README.html) | ||
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| [](http://www.repostatus.org/#active) | ||
| [](https://codecov.io/gh/GuangchuangYu/ReactomePA/) | ||
| [)`-green.svg)](https://github.com/GuangchuangYu/ReactomePA/commits/master) | ||
| [](https://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#svn_source) | ||
| [](https://github.com/GuangchuangYu/ReactomePA/network) | ||
| [](https://github.com/GuangchuangYu/ReactomePA/stargazers) | ||
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||
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| [![releaseVersion](https://img.shields.io/badge/release%20version-`r url="https://bioconductor.org/packages/release/bioc/html/ReactomePA.html"; x=readLines(url); gsub("\\D+(\\d+\\.\\d+\\.\\d+)\\D+", "\\1", x[grep("Version", x) +1])`-green.svg?style=flat)](https://bioconductor.org/packages/ReactomePA) | ||
| [![develVersion](https://img.shields.io/badge/devel%20version-`r x=readLines("DESCRIPTION"); y=x[grep("^Version", x)]; sub("Version: ", "", y)`-green.svg?style=flat)](https://github.com/GuangchuangYu/ReactomePA) | ||
| [](https://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#since) | ||
| [](https://support.bioconductor.org/t/ReactomePA/) | ||
| [](https://bioconductor.org/packages/stats/bioc/ReactomePA/) | ||
|
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||
|
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| This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. | ||
|
|
||
| [](https://twitter.com/intent/tweet?hashtags=ReactomePA&url=https://guangchuangyu.github.io/ReactomePA) | ||
|
|
||
| ------------------------------------------------------------------------ | ||
|
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| Please cite the following article when using `ReactomePA`: | ||
|
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| __*G Yu*__, QY He^\*^. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. __*Molecular BioSystems*__ 2016, 12(2):477-479. | ||
|
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||
| [](http://dx.doi.org/1039/c5mb00663e) | ||
| [; sum(get_article_cite_history('DO5oG40AAAAJ', '8d8msizDQcsC')$cites)`-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=16627502277303919270,2188293597650690793,16774578204592269646,17800543858983923015) | ||
|
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| ------------------------------------------------------------------------ | ||
|
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| For details, please visit our project website, <https://guangchuangyu.github.io/ReactomePA>. | ||
|
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||
| + [Documentation](https://guangchuangyu.github.io/ReactomePA/documentation/) | ||
| + [Featured Articles](https://guangchuangyu.github.io/ReactomePA/featuredArticles/) | ||
| + [Feedback](https://guangchuangyu.github.io/ReactomePA/#feedback) | ||
|
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| ### Citation | ||
|
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||
| [; sum(get_article_cite_history('DO5oG40AAAAJ', '8d8msizDQcsC')$cites)`-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=3311691878690959578) | ||
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| ```{r echo=F, comment=NA} | ||
| d <- scholar::get_article_cite_history('DO5oG40AAAAJ', '8d8msizDQcsC') | ||
| txtplot::txtplot(d$year, d$cites) | ||
| ``` | ||
|
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| ### Download stats | ||
|
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| [](https://bioconductor.org/packages/stats/bioc/ReactomePA/) | ||
| [![total](https://img.shields.io/badge/downloads-`r sum(dlstats::bioc_stats("ReactomePA")$Nb_of_downloads)`/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ReactomePA/) | ||
| [![month](https://img.shields.io/badge/downloads-`r x <- dlstats::bioc_stats("ReactomePA"); x$Nb_of_downloads[nrow(x)-1]`/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ReactomePA/) | ||
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| ```{r echo=F, comment=NA} | ||
| x <- dlstats::bioc_stats("ReactomePA") | ||
| x <- x[-nrow(x), ] # last month data is not complete | ||
| txtplot::txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25) | ||
| ``` | ||
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||
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| # ReactomePA: Reactome Pathway Analysis | ||
| ReactomePA: Reactome Pathway Analysis | ||
| ===================================== | ||
|
|
||
| [](https://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#archives) | ||
| [](https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomePA/) | ||
| [](https://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#since) | ||
| [](https://support.bioconductor.org/t/ReactomePA/) | ||
| [](https://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#svn_source) | ||
| [](https://bioconductor.org/packages/stats/bioc/ReactomePA) | ||
| [](https://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#archives) [](https://bioconductor.org/checkResults/devel/bioc-LATEST/ReactomePA/) [](https://travis-ci.org/GuangchuangYu/ReactomePA) [](https://ci.appveyor.com/project/GuangchuangYu/ReactomePA) [](http://bioconda.github.io/recipes/bioconductor-reactomepa/README.html) | ||
|
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| [](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ReactomePA/) [](https://github.com/GuangchuangYu/ReactomePA/commits/master) [](https://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#svn_source) [](https://github.com/GuangchuangYu/ReactomePA/network) [](https://github.com/GuangchuangYu/ReactomePA/stargazers) | ||
|
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||
| [](https://bioconductor.org/packages/ReactomePA) [](https://github.com/GuangchuangYu/ReactomePA) [](https://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html#since) [](https://support.bioconductor.org/t/ReactomePA/) [](https://bioconductor.org/packages/stats/bioc/ReactomePA/) | ||
|
|
||
| This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. | ||
|
|
||
| [](https://twitter.com/intent/tweet?hashtags=ReactomePA&url=https://guangchuangyu.github.io/ReactomePA) | ||
|
|
||
| ------------------------------------------------------------------------ | ||
|
|
||
| Please cite the following article when using `ReactomePA`: | ||
|
|
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| ***G Yu***, QY He<sup>\*</sup>. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. ***Molecular BioSystems*** 2016, 12(2):477-479. | ||
|
|
||
| [](http://dx.doi.org/1039/c5mb00663e) [](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=16627502277303919270,2188293597650690793,16774578204592269646,17800543858983923015) | ||
|
|
||
| ------------------------------------------------------------------------ | ||
|
|
||
| For details, please visit our project website, <https://guangchuangyu.github.io/ReactomePA>. | ||
|
|
||
| - [Documentation](https://guangchuangyu.github.io/ReactomePA/documentation/) | ||
| - [Featured Articles](https://guangchuangyu.github.io/ReactomePA/featuredArticles/) | ||
| - [Feedback](https://guangchuangyu.github.io/ReactomePA/#feedback) | ||
|
|
||
| ### Citation | ||
|
|
||
| [](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=3311691878690959578) | ||
|
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| +-+---------+---------+---------+---------+--------+---+ | ||
| 4 + * + | ||
| | | | ||
| 3.5 + + | ||
| | | | ||
| 3 + + | ||
| | | | ||
| 2.5 + + | ||
| 2 + + | ||
| | | | ||
| 1.5 + + | ||
| | | | ||
| 1 + * + | ||
| +-+---------+---------+---------+---------+--------+---+ | ||
| 2015 2015.2 2015.4 2015.6 2015.8 2016 | ||
|
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| ### Download stats | ||
|
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| [](https://bioconductor.org/packages/stats/bioc/ReactomePA/) [](https://bioconductor.org/packages/stats/bioc/ReactomePA/) [](https://bioconductor.org/packages/stats/bioc/ReactomePA/) | ||
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| +------------------+-------------------+------------------+-------------------+----------------+ | ||
| | * | | ||
| | | | ||
| 800 + + | ||
| | | | ||
| | * | | ||
| | * * | | ||
| | * | | ||
| 600 + * * * + | ||
| | * * * | | ||
| | * * * * | | ||
| | * ** * ** * * * | | ||
| | * * * * | | ||
| 400 + * * * * * * + | ||
| | * * * * | | ||
| | * | | ||
| | ** * * | | ||
| 200 + * * * ** + | ||
| | * ** | | ||
| | * | | ||
| | | | ||
| | | | ||
| 0 + * + | ||
| +------------------+-------------------+------------------+-------------------+----------------+ | ||
| 2013 2014 2015 2016 |
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| environment: | ||
| matrix: | ||
| - R_VERSION: devel | ||
| R_ARCH: x64 | ||
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| # DO NOT CHANGE the "init" and "install" sections below | ||
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| # 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 | ||
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| # Adapt as necessary starting from here | ||
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| build_script: | ||
| - travis-tool.sh install_bioc BiocStyle AnnotationDbi DO.db org.Hs.eg.db reactome.db | ||
| - travis-tool.sh install_deps | ||
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| test_script: | ||
| - travis-tool.sh run_tests | ||
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| on_failure: | ||
| - 7z a failure.zip *.Rcheck\* | ||
| - appveyor PushArtifact failure.zip | ||
|
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| artifacts: | ||
| - path: '*.Rcheck\**\*.log' | ||
| name: Logs | ||
|
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| - path: '*.Rcheck\**\*.out' | ||
| name: Logs | ||
|
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| - path: '*.Rcheck\**\*.fail' | ||
| name: Logs | ||
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| - path: '*.Rcheck\**\*.Rout' | ||
| name: Logs | ||
|
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| - path: '\*_*.tar.gz' | ||
| name: Linux Package | ||
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| - path: '\*_*.zip' | ||
| name: Windows Package | ||
|
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| notifications: | ||
| - provider: Email | ||
| to: | ||
| - [email protected] | ||
| on_build_success: false | ||
|
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| library(testthat) | ||
| library(ReactomePA) | ||
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| test_check("ReactomePA") | ||
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| library(ReactomePA) | ||
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| context("getDb") | ||
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| test_that("getDb", { | ||
| expect_equal(getDb("human"), "org.Hs.eg.db") | ||
| expect_equal(getDb("mouse"), "org.Mm.eg.db") | ||
| }) | ||
|
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