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README.md
# iSEEde <!-- badges: start --> [![GitHub issues](https://img.shields.io/github/issues/iSEE/iSEEde)](https://github.com/iSEE/iSEEde/issues) [![GitHub pulls](https://img.shields.io/github/issues-pr/iSEE/iSEEde)](https://github.com/iSEE/iSEEde/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/iSEEde/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/iSEE/iSEEde/actions) [![Codecov test coverage](https://codecov.io/gh/iSEE/iSEEde/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/iSEE/iSEEde?branch=devel) <!-- badges: end --> The goal of *[iSEEde](https://bioconductor.org/packages/iSEEde)* is to provide panels that facilitate the interactive visualisation of differential expression results in *[iSEE](https://bioconductor.org/packages/iSEE)* applications. ## Installation instructions Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install *[iSEEde](https://bioconductor.org/packages/iSEEde)* from [Bioconductor](http://bioconductor.org/) using the following code: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("iSEEde") ``` And the bleeding edge development version from [GitHub](https://github.com/iSEE/iSEEde) with: ``` r BiocManager::install("iSEE/iSEEde") ``` ## Example This is a basic example which shows you how to interactively explore differential expression results for an example data set in an *[iSEE](https://bioconductor.org/packages/iSEE)* application, using designated panels implemented in *[iSEEde](https://bioconductor.org/packages/iSEEde)*: ``` r library("iSEEde") library("airway") library("DESeq2") library("iSEE") # Example data ---- data("airway") airway$dex <- relevel(airway$dex, "untrt") dds <- DESeqDataSet(airway, ~ 0 + dex + cell) dds <- DESeq(dds) res_deseq2 <- results(dds, contrast = list("dextrt", "dexuntrt")) # iSEE / iSEEde --- airway <- embedContrastResults(res_deseq2, airway, name = "dex: trt vs untrt") app <- iSEE(airway, initial = list( DETable(ContrastName="dex: trt vs untrt", HiddenColumns = c("baseMean", "lfcSE", "stat"), PanelWidth = 4L), VolcanoPlot(ContrastName="dex: trt vs untrt", PanelWidth = 4L), MAPlot(ContrastName="dex: trt vs untrt", PanelWidth = 4L) )) if (interactive()) { shiny::runApp(app) } ``` ## Citation Below is the citation output from using `citation('iSEEde')` in R. Please run this yourself to check for any updates on how to cite **iSEEde**. ``` r print(citation("iSEEde"), bibtex = TRUE) #> #> To cite package 'iSEEde' in publications use: #> #> Rue-Albrecht K (2022). _iSEEde: iSEE extension for panels related to #> differential expression analysis_. R package version 0.99.0, #> <https://github.com/iSEE/iSEEde>. #> #> A BibTeX entry for LaTeX users is #> #> @Manual{, #> title = {iSEEde: iSEE extension for panels related to differential expression analysis}, #> author = {Kevin Rue-Albrecht}, #> year = {2022}, #> note = {R package version 0.99.0}, #> url = {https://github.com/iSEE/iSEEde}, #> } ``` Please note that the *[iSEEde](https://bioconductor.org/packages/iSEEde)* 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 *[iSEEde](https://bioconductor.org/packages/iSEEde)* 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/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/iSEEde) 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/biocthis)*. ## Code of Conduct Please note that the iSEEde 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.