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README.md
<!-- README.md is generated from README.Rmd. Please edit that file --> # iSEEpathways <!-- badges: start --> [![GitHub issues](https://img.shields.io/github/issues/iSEE/iSEEpathways)](https://github.com/iSEE/iSEEpathways/issues) [![GitHub pulls](https://img.shields.io/github/issues-pr/iSEE/iSEEpathways)](https://github.com/iSEE/iSEEpathways/pulls) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![R-CMD-check-bioc](https://github.com/iSEE/iSEEpathways/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/iSEE/iSEEpathways/actions) [![Codecov test coverage](https://codecov.io/gh/iSEE/iSEEpathways/branch/main/graph/badge.svg)](https://app.codecov.io/gh/iSEE/iSEEpathways?branch=main) <!-- badges: end --> The goal of `iSEEpathways` is to provide panels to facilitate the interactive visualisation of pathway analysis results in *[iSEE](https://bioconductor.org/packages/3.18/iSEE)* applications. ## Installation instructions Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `iSEEpathways` from [Bioconductor](http://bioconductor.org/) using the following code: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("iSEEpathways") ``` And the development version from [GitHub](https://github.com/iSEE/iSEEpathways) with: ``` r BiocManager::install("iSEE/iSEEpathways") ``` ## Example This is a basic example which shows you how to load the package: ``` r library("iSEEpathways") library("fgsea") library("iSEE") # Example data ---- simulated_data <- simulateExampleData() pathways_list <- simulated_data[["pathwaysList"]] features_stat <- simulated_data[["featuresStat"]] se <- simulated_data[["summarizedexperiment"]] # fgsea ---- set.seed(42) fgseaRes <- fgsea(pathways = pathways_list, stats = features_stat, minSize = 15, maxSize = 500) fgseaRes <- fgseaRes[order(pval), ] head(fgseaRes) #> pathway pval padj log2err ES NES size #> 1: pathway_1350 0.0004373110 0.5905978 0.4984931 0.2858201 1.503211 299 #> 2: pathway_4907 0.0005947840 0.5905978 0.4772708 0.3250965 1.599638 178 #> 3: pathway_3983 0.0007509197 0.5905978 0.4772708 0.2558001 1.398213 451 #> 4: pathway_398 0.0008716489 0.5905978 0.4772708 0.2799932 1.477849 305 #> 5: pathway_3359 0.0009809867 0.5905978 0.4550599 -0.3724340 -1.674911 106 #> 6: pathway_1289 0.0009835850 0.5905978 0.4550599 0.3479133 1.638048 124 #> leadingEdge #> 1: feature_6060,feature_9203,feature_1852,feature_1883,feature_12903,feature_2143,... #> 2: feature_9265,feature_6286,feature_14879,feature_9600,feature_5335,feature_12205,... #> 3: feature_495,feature_12466,feature_13128,feature_3069,feature_5278,feature_4248,... #> 4: feature_6478,feature_2164,feature_922,feature_4298,feature_6585,feature_1633,... #> 5: feature_3879,feature_2726,feature_6870,feature_6787,feature_9700,feature_693,... #> 6: feature_6376,feature_12953,feature_8391,feature_3147,feature_7330,feature_11551,... # iSEE --- se <- embedPathwaysResults(fgseaRes, se, name = "fgsea", class = "fgsea", pathwayType = "simulated", pathwaysList = pathways_list, featuresStats = features_stat) app <- iSEE(se, initial = list( PathwaysTable(ResultName="fgsea", Selected = "pathway_3363 ", PanelWidth = 6L), FgseaEnrichmentPlot(ResultName="fgsea", PathwayId = "pathway_3363", PanelWidth = 6L) )) if (interactive()) { shiny::runApp(app) } ``` ## Citation Below is the citation output from using `citation('iSEEpathways')` in R. Please run this yourself to check for any updates on how to cite **iSEEpathways**. ``` r print(citation('iSEEpathways'), bibtex = TRUE) #> To cite package 'iSEEpathways' in publications use: #> #> Rue-Albrecht K (2023). _iSEEpathways: iSEE extension for panels #> related to pathway analysis_. R package version 0.99.0, #> <https://github.com/iSEE/iSEEpathways>. #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> title = {iSEEpathways: iSEE extension for panels related to pathway analysis}, #> author = {Kevin Rue-Albrecht}, #> year = {2023}, #> note = {R package version 0.99.0}, #> url = {https://github.com/iSEE/iSEEpathways}, #> } ``` Please note that the `iSEEpathways` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package. ## Code of Conduct Please note that the `iSEEpathways` project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms. ## Development tools - Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/) through *[usethis](https://CRAN.R-project.org/package=usethis)*, *[remotes](https://CRAN.R-project.org/package=remotes)*, and *[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized to use [Bioconductor’s docker containers](https://www.bioconductor.org/help/docker/) and *[BiocCheck](https://bioconductor.org/packages/3.18/BiocCheck)*. - Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and *[covr](https://CRAN.R-project.org/package=covr)*. - The [documentation website](http://iSEE.github.io/iSEEpathways) is automatically updated thanks to *[pkgdown](https://CRAN.R-project.org/package=pkgdown)*. - The code is styled automatically thanks to *[styler](https://CRAN.R-project.org/package=styler)*. - The documentation is formatted thanks to *[devtools](https://CRAN.R-project.org/package=devtools)* and *[roxygen2](https://CRAN.R-project.org/package=roxygen2)*. For more details, check the `dev` directory. This package was developed using *[biocthis](https://bioconductor.org/packages/3.18/biocthis)*. ## Code of Conduct Please note that the iSEEpathways project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.