diff --git a/README.md b/README.md index 9ddc70f..11f5d27 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,23 @@ # atena: analysis of transposable elements in R and Bioconductor -[![R-CMD-check-bioc](https://github.com/functionalgenomics/atena/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/functionalgenomics/atena/actions?query=workflow%3AR-CMD-check-bioc) -[![Support posts](https://bioconductor.org/shields/posts/atena.svg)](https://support.bioconductor.org/t/atena/ "Support site activity on atena, last 6 months: tagged questions/avg. answers per question/avg. comments per question/accepted answers, or 0 if no tagged posts.") -[![Codecov test coverage](https://codecov.io/gh/functionalgenomics/atena/branch/master/graph/badge.svg?token=kJ4Hww6UHl)](https://codecov.io/gh/functionalgenomics/atena) - -This `atena` package provides access from R/Bioconductor to the following +[![Bioconductor Time](https://bioconductor.org/shields/years-in-bioc/atena.svg)](https://bioconductor.org/packages/release/bioc/html/atean.html "How long has been atena in a release of Bioconductor") +[![Bioconductor Downloads](https://bioconductor.org/shields/downloads/release/atena.svg)](https://bioconductor.org/packages/stats/bioc/atena/ "Ranking by number of downloads. A lower number means the package is downloaded more frequently. Determined within a package type (software, experiment, annotation, workflow) and uses the number of distinct IPs for the last 12 months.") +[![Support posts](https://bioconductor.org/shields/posts/atena.svg)](https://support.bioconductor.org/t/atena/ "Support site activity on atena, last 6 months: answered posts/total posts.") +[![R-CMD-check-bioc](https://github.com/rcastelo/atena/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/rcastelo/atena/actions?query=workflow%3AR-CMD-check-bioc) +[![codecov.io](https://codecov.io/github/rcastelo/atena/coverage.svg?branch=devel)](https://app.codecov.io/github/rcastelo/atena?branch=devel) + + +**Current Bioconductor build status** +- `release` [![Bioconductor Availability](https://bioconductor.org/shields/availability/release/atena.svg)](https://bioconductor.org/packages/release/bioc/html/atena.html#archives "Whether atena release is available on all platforms") +[![Bioconductor Dependencies](https://bioconductor.org/shields/dependencies/release/atena.svg)](https://bioconductor.org/packages/release/bioc/html/atena.html#since "Number of recursive dependencies needed to install package") +[![Bioconductor Commits](https://bioconductor.org/shields/lastcommit/release/bioc/atena.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/atena "Time since last commit, possible values: today, < 1 week, < 1 month, < 3 months, since release, before release") +[![Bioconductor Release Build](https://bioconductor.org/shields/build/release/bioc/atena.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/atena/ "Bioconductor release build") +- `development` [![Bioconductor Availability](https://bioconductor.org/shields/availability/devel/atena.svg)](https://bioconductor.org/packages/devel/bioc/html/atena.html#archives "Whether atena devel is available on all platforms") +[![Bioconductor Dependencies](https://bioconductor.org/shields/dependencies/devel/atena.svg)](https://bioconductor.org/packages/devel/bioc/html/atena.html#since "Number of recursive dependencies needed to install package") +[![Bioconductor Commits](https://bioconductor.org/shields/lastcommit/devel/bioc/atena.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/atena "Time since last commit, possible values: today, < 1 week, < 1 month, < 3 months, since release, before release") +[![Bioconductor Devel Build](https://bioconductor.org/shields/build/devel/bioc/atena.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/atena/ "Bioconductor devel build") + +The `atena` package provides access from R/Bioconductor to the following methods for the quantification of transposable element (TE) expression: * Jin Y et al. TEtranscripts: a package for including transposable elements @@ -21,44 +34,47 @@ methods for the quantification of transposable element (TE) expression: PLOS Comp. Biol. 2019;15(9):e1006453. DOI: [10.1371/journal.pcbi.1006453](https://doi.org/10.1371/journal.pcbi.1006453). - ## Installation `atena` has been submitted to Bioconductor. -To install the __release__ version of this package please go to its package release landing page at [https://bioconductor.org/packages/atena](https://bioconductor.org/packages/atena) and follow the instructions there to install it. +To install the __release__ version of this package please go to its package +release landing page at +[https://bioconductor.org/packages/atena](https://bioconductor.org/packages/atena) +and follow the instructions there to install it. -This github repository contains the __development__ version of the R/Bioconductor package `atena`. This version is unstable and should be used only to test new features. -To install the development version you first need to install the [development version of Bioconductor](https://bioconductor.org/developers/how-to/useDevel) and then type the following line from the R shell: +This github repository contains the __development__ version of the +R/Bioconductor package `atena`. This version is unstable and should be used +only to test new features. To install the development version you first need to +install the +[development version of Bioconductor](https://bioconductor.org/developers/how-to/useDevel) +and then type the following line from the R shell: ```r -BiocManager::install("atena", version = "devel") +BiocManager::install("atena", version="devel") ``` -Alternatively, you can install it from this GitHub repo using the [remotes](https://cran.r-project.org/package=remotes) package, as follows: +Alternatively, you can directly install it from this GitHub repo as follows: ``` -library(remotes) - -install_github("functionalgenomics/atena") +BiocManager::install("rcastelo/atena") ``` -Provided that you have installed first all its Bioconductor dependencies; -see the `DESCRIPTION` file. The vignette contains an example on how to use it. - - ## Questions, bug reports and issues For questions and bug reports regarding the __release__ version of **atena** -please use the [Bioconductor support site](https://support.bioconductor.org "Bioconductor support site"). +please use the +[Bioconductor support site](https://support.bioconductor.org "Bioconductor support site"). For bug reports and issues regarding this __development__ version of **atena** -please use the GitHub issues [tab](https://github.com/functionalgenomics/atena/issues) at the top-left of this page. +please use the GitHub issues [tab](https://github.com/rcastelo/atena/issues) at +the top-left of this page. ## Contributing -Contributions to the software codebase of atena are welcome as long as contributors abide to the -terms of the [Bioconductor Contributor Code of Conduct](https://bioconductor.org/about/code-of-conduct). +Contributions to the software codebase of atena are welcome as long as +contributors abide to the terms of the +[Bioconductor Contributor Code of Conduct](https://bioconductor.org/about/code-of-conduct). If you want to contribute to the development of GenomicScores please open an -[issue](https://github.com/functionalgenomics/atena/issues) to start discussing your suggestion or, in case of a -bugfix or a straightforward feature, directly a -[pull request](https://github.com/functionalgenomics/atena/pulls). +[issue](https://github.com/rcastelo/atena/issues) to start discussing your +suggestion or, in case of a bugfix or a straightforward feature, directly a +[pull request](https://github.com/rcastelo/atena/pulls).