From 67016db832fcb63ab75e24a8c8d26de7bad66845 Mon Sep 17 00:00:00 2001 From: Kevin Rue-Albrecht Date: Fri, 1 Nov 2024 10:01:54 +0000 Subject: [PATCH] remove links specific to release 3.16 and update text --- README.Rmd | 111 ----------------------------------------------------- README.md | 27 ++++++------- 2 files changed, 14 insertions(+), 124 deletions(-) delete mode 100644 README.Rmd diff --git a/README.Rmd b/README.Rmd deleted file mode 100644 index 5ad421a..0000000 --- a/README.Rmd +++ /dev/null @@ -1,111 +0,0 @@ ---- -output: github_document ---- - - - -```{r, include = FALSE} -knitr::opts_chunk$set( - collapse = TRUE, - comment = "#>", - fig.path = "man/figures/README-", - out.width = "100%" -) -``` - -# iSEEde - - -[![GitHub issues](https://img.shields.io/github/issues/iSEE/iSEEde)](https://github.com/iSEE/iSEEde/issues) -[![GitHub pulls](https://img.shields.io/github/issues-pr/iSEE/iSEEde)](https://github.com/iSEE/iSEEde/pulls) -[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -[![R-CMD-check-bioc](https://github.com/iSEE/iSEEde/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/iSEE/iSEEde/actions) -[![Codecov test coverage](https://codecov.io/gh/iSEE/iSEEde/branch/main/graph/badge.svg)](https://app.codecov.io/gh/iSEE/iSEEde?branch=main) - - -The goal of `r BiocStyle::Biocpkg("iSEEde")` is to provide panels that facilitate the interactive visualisation of differential expression results in `r BiocStyle::Biocpkg("iSEE")` applications. - -## Installation instructions - -Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `r BiocStyle::Biocpkg("iSEEde")` from [Bioconductor](http://bioconductor.org/) using the following code: - -```{r 'install', eval = FALSE} -if (!requireNamespace("BiocManager", quietly = TRUE)) { - install.packages("BiocManager") -} - -BiocManager::install("iSEEde") -``` - -And the development version from [GitHub](https://github.com/iSEE/iSEEde) with: - -```{r 'install_dev', eval = FALSE} -BiocManager::install("iSEE/iSEEde") -``` - -## Example - -This is a basic example which shows you how to load the package: - -```{r example, message=FALSE, warning=FALSE, eval = requireNamespace('iSEEde')} -library("iSEEde") -library("airway") -library("DESeq2") -library("iSEE") - -# Example data ---- - -data("airway") -airway$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 'citation', eval = requireNamespace('iSEEde')} -print(citation("iSEEde"), bibtex = TRUE) -``` - -Please note that the `r BiocStyle::Biocpkg("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 `r BiocStyle::Biocpkg("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 `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`. -* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`. -* The [documentation website](http://iSEE.github.io/iSEEde) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`. -* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`. -* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`. - -For more details, check the `dev` directory. - -This package was developed using `r BiocStyle::Biocpkg('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. diff --git a/README.md b/README.md index f4830b6..52ce625 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,3 @@ - - - # iSEEde @@ -13,19 +10,19 @@ pulls](https://img.shields.io/github/issues-pr/iSEE/iSEEde)](https://github.com/ 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/main/graph/badge.svg)](https://app.codecov.io/gh/iSEE/iSEEde?branch=main) +coverage](https://codecov.io/gh/iSEE/iSEEde/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/iSEE/iSEEde?branch=devel) -The goal of *[iSEEde](https://bioconductor.org/packages/3.16/iSEEde)* is +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/3.16/iSEE)* applications. +*[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/3.16/iSEEde)* from +*[iSEEde](https://bioconductor.org/packages/iSEEde)* from [Bioconductor](http://bioconductor.org/) using the following code: ``` r @@ -36,7 +33,7 @@ if (!requireNamespace("BiocManager", quietly = TRUE)) { BiocManager::install("iSEEde") ``` -And the development version from +And the bleeding edge development version from [GitHub](https://github.com/iSEE/iSEEde) with: ``` r @@ -45,7 +42,11 @@ BiocManager::install("iSEE/iSEEde") ## Example -This is a basic example which shows you how to load the package: +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") @@ -106,7 +107,7 @@ print(citation("iSEEde"), bibtex = TRUE) ``` Please note that the -*[iSEEde](https://bioconductor.org/packages/3.16/iSEEde)* was only made +*[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. @@ -114,7 +115,7 @@ this package. ## Code of Conduct Please note that the -*[iSEEde](https://bioconductor.org/packages/3.16/iSEEde)* project is +*[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. @@ -128,7 +129,7 @@ contributing to this project, you agree to abide by its terms. *[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/3.16/BiocCheck)*. + *[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)*. @@ -144,7 +145,7 @@ contributing to this project, you agree to abide by its terms. For more details, check the `dev` directory. This package was developed using -*[biocthis](https://bioconductor.org/packages/3.16/biocthis)*. +*[biocthis](https://bioconductor.org/packages/biocthis)*. ## Code of Conduct