Updated README.md

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)
+<img align="right" src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/atena/atena.png" height="200"/>
+
+**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).