@@ -3,9 +3,12 @@
                                      [![Bioconductor Time](https://bioconductor.org/shields/years-in-bioc/GSVA.svg)](https://bioconductor.org/packages/release/bioc/html/GSVA.html "How long has been GSVA in a release of Bioconductor")
                                      [![Bioconductor Downloads](https://bioconductor.org/shields/downloads/release/GSVA.svg)](https://bioconductor.org/packages/stats/bioc/GSVA/ "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/GSVA.svg)](https://support.bioconductor.org/t/GSVA/ "Support site activity on GSVA, last 6 months: answered posts/total posts.")
                                     +[![R-CMD-check-bioc](https://github.com/rcastelo/GSVA/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/rcastelo/GSVA/actions?query=workflow%3AR-CMD-check-bioc)
                                     +[![codecov.io](https://codecov.io/github/rcastelo/GSVA/coverage.svg?branch=master)](https://codecov.io/github/rcastelo/GSVA?branch=master)
                                      <img align="right" src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/GSVA/GSVA.png" height="200"/>
                                     -**Current build status**
+                                    +
                                     +**Current Bioconductor build status**
                                      - `release` [![Bioconductor Availability](https://bioconductor.org/shields/availability/release/GSVA.svg)](https://bioconductor.org/packages/release/bioc/html/GSVA.html#archives "Whether GSVA release is available on all platforms")
                                      [![Bioconductor Dependencies](https://bioconductor.org/shields/dependencies/release/GSVA.svg)](https://bioconductor.org/packages/release/bioc/html/GSVA.html#since "Number of recursive dependencies needed to install package")
                                      [![Bioconductor Commits](https://bioconductor.org/shields/lastcommit/release/bioc/GSVA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/GSVA "Time since last commit, possible values: today, < 1 week, < 1 month, < 3 months, since release, before release")

@@ -42,7 +42,7 @@ install_github("rcastelo/GSVA")
                                      For questions and bug reports regarding the __release__ version of **GSVA**
                                      please use the [Bioconductor support site](https://support.bioconductor.org "Bioconductor support site").
                                      For feature requests or bug reports and issues regarding this __development__ version of **GSVA**
                                     -please use the GitHub issues [tab](https://github.com/rcastelo/GSVA/issues)) at the top-left of this page.
                                     +please use the GitHub issues [tab](https://github.com/rcastelo/GSVA/issues) at the top-left of this page.
                                      ## Contributing

@@ -23,8 +23,7 @@ The `GSVA` package allows one to perform a change in coordinate systems of molec
                                      This is the __development__ version of the R/Bioconductor package GSVA. This version is unstable and should be used only to test new features. If you are looking for the __release__ version of this package please go to its package release landing page at [https://bioconductor.org/packages/GSVA](https://bioconductor.org/packages/GSVA) and follow the instructions there to install it.
                                     -If you were really looking for this development version, then to install it you
                                     -need first to install the development version of Bioconductor following the instructions at [http://bioconductor.org/developers/how-to/useDevel](http://bioconductor.org/developers/how-to/useDevel) and then type the following line from the R shell:
                                     +If you were really looking for this development version, then to install it you need first 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("GSVA", version = "devel")

@@ -31,11 +31,11 @@ install.packages("BiocManager")
                                      BiocManager::install("GSVA", version = "devel")
                                      ```
                                     -Alternatively, you can install it from GitHub using the [devtools](https://github.com/hadley/devtools "devtools") package.
                                     +Alternatively, you can install it from GitHub using the [remotes](https://github.com/r-lib/remotes "remotes") package.
                                      ```r
                                     -install.packages("devtools")
                                     -library(devtools)
                                     +install.packages("remotes")
                                     +library(remotes)
                                      install_github("rcastelo/GSVA")
                                      ```
@@ -46,3 +46,12 @@ please use the [Bioconductor support site](https://support.bioconductor.org "Bio
                                      For feature requests or bug reports and issues regarding this __development__ version of **GSVA**
                                      please use the GitHub issues link at the top-right of this page
                                      ([https://github.com/rcastelo/GSVA/issues](https://github.com/rcastelo/GSVA/issues)).
+                                    +
                                     +## Contributing
+                                    +
                                     +Contributions to the software codebase of GSVA 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 GSVA please open an
                                     +[issue](https://github.com/rcastelo/GSVA/issues) to start discussing your suggestion or, in case of a
                                     +bugfix or a straightforward feature, directly a
                                     +[pull request](https://github.com/rcastelo/GSVA/pulls).

@@ -2,17 +2,18 @@
                                      [![Bioconductor Time](https://bioconductor.org/shields/years-in-bioc/GSVA.svg)](https://bioconductor.org/packages/release/bioc/html/GSVA.html "How long has been GSVA in a release of Bioconductor")
                                      [![Bioconductor Downloads](https://bioconductor.org/shields/downloads/GSVA.svg)](https://bioconductor.org/packages/stats/bioc/GSVA/ "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")
                                     -[![Bioconductor Commits](https://bioconductor.org/shields/lastcommit/release/bioc/GSVA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/GSVA "Time since last commit, possible values: today, < 1 week, < 1 month, < 3 months, since release, before release")
                                      [![Support posts](https://bioconductor.org/shields/posts/GSVA.svg)](https://support.bioconductor.org/t/GSVA/ "Support site activity on GSVA, last 6 months: tagged questions/avg. answers per question/avg. comments per question/accepted answers, or 0 if no tagged posts.")
                                      <img align="right" src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/GSVA/GSVA.png" height="200"/>
                                      **Current build status**
                                      - `release` [![Bioconductor Availability](https://bioconductor.org/shields/availability/release/GSVA.svg)](https://bioconductor.org/packages/release/bioc/html/GSVA.html#archives "Whether GSVA release is available on all platforms")
                                     -[![Bioconductor Release Build](https://bioconductor.org/shields/build/release/bioc/GSVA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/GSVA/ "Bioconductor release build")
                                      [![Bioconductor Dependencies](https://bioconductor.org/shields/dependencies/release/GSVA.svg)](https://bioconductor.org/packages/release/bioc/html/GSVA.html#since "Number of recursive dependencies needed to install package")
                                     +[![Bioconductor Commits](https://bioconductor.org/shields/lastcommit/release/bioc/GSVA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/GSVA "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/GSVA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/GSVA/ "Bioconductor release build")
                                      - `development` [![Bioconductor Availability](https://bioconductor.org/shields/availability/devel/GSVA.svg)](https://bioconductor.org/packages/devel/bioc/html/GSVA.html#archives "Whether GSVA devel is available on all platforms")
                                     -[![Bioconductor Devel Build](https://bioconductor.org/shields/build/devel/bioc/GSVA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/GSVA/ "Bioconductor devel build")
                                      [![Bioconductor Dependencies](https://bioconductor.org/shields/dependencies/devel/GSVA.svg)](https://bioconductor.org/packages/devel/bioc/html/GSVA.html#since "Number of recursive dependencies needed to install package")
                                     +[![Bioconductor Commits](https://bioconductor.org/shields/lastcommit/devel/bioc/GSVA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/GSVA "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/GSVA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/GSVA/ "Bioconductor devel build")
                                      The `GSVA` package allows one to perform a change in coordinate systems of molecular measurements, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods such as functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. For citing `GSVA` as a software package, please use the following reference:

@@ -1,16 +1,18 @@
                                      # GSVA: gene set variation analysis for microarray and RNA-seq data
                                     -[![Bioconductor Time](http://bioconductor.org/shields/years-in-bioc/GSVA.svg)](http://bioconductor.org/packages/release/bioc/html/GSVA.html "How long has been GSVA in a release of Bioconductor")
                                     -[![Bioconductor Downloads](http://bioconductor.org/shields/downloads/GSVA.svg)](http://bioconductor.org/packages/stats/bioc/GSVA/ "Percentile (top 5/20/50% or 'available') of downloads over the last 6 full months")
                                     -[![Bioconductor Commits](http://bioconductor.org/shields/commits/bioc/GSVA.svg)](http://bioconductor.org/packages/devel/bioc/html/GSVA.html#svn_source "Average SVN commits (to the devel branch) per month over the last 6 months")
                                     -[![Support posts](http://bioconductor.org/shields/posts/GSVA.svg)](https://support.bioconductor.org/t/GSVA/ "Bioconductor support site activity on GSVA, last 6 months: tagged questions/avg. answers per question/avg. comments per question/accepted answers, or 0 if no tagged posts.")
                                     +[![Bioconductor Time](https://bioconductor.org/shields/years-in-bioc/GSVA.svg)](https://bioconductor.org/packages/release/bioc/html/GSVA.html "How long has been GSVA in a release of Bioconductor")
                                     +[![Bioconductor Downloads](https://bioconductor.org/shields/downloads/GSVA.svg)](https://bioconductor.org/packages/stats/bioc/GSVA/ "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")
                                     +[![Bioconductor Commits](https://bioconductor.org/shields/lastcommit/release/bioc/GSVA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/GSVA "Time since last commit, possible values: today, < 1 week, < 1 month, < 3 months, since release, before release")
                                     +[![Support posts](https://bioconductor.org/shields/posts/GSVA.svg)](https://support.bioconductor.org/t/GSVA/ "Support site activity on GSVA, last 6 months: tagged questions/avg. answers per question/avg. comments per question/accepted answers, or 0 if no tagged posts.")
                                      <img align="right" src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/GSVA/GSVA.png" height="200"/>
                                      **Current build status**
                                      - `release` [![Bioconductor Availability](http://bioconductor.org/shields/availability/release/GSVA.svg)](http://bioconductor.org/packages/release/bioc/html/GSVA.html#archives "Whether GSVA release is available on all platforms")
                                      [![Bioconductor Release Build](http://bioconductor.org/shields/build/release/bioc/GSVA.svg)](http://bioconductor.org/checkResults/release/bioc-LATEST/GSVA/ "Bioconductor release build")
                                     +[![Bioconductor Dependencies](http://bioconductor.org/shields/dependencies/release/GSVA.svg)](http://bioconductor.org/packages/release/bioc/html/GSVA.html#since "Number of recursive dependencies needed to install package")
                                      - `development` [![Bioconductor Availability](http://bioconductor.org/shields/availability/devel/GSVA.svg)](http://bioconductor.org/packages/devel/bioc/html/GSVA.html#archives "Whether GSVA devel is available on all platforms")
                                      [![Bioconductor Devel Build](http://bioconductor.org/shields/build/devel/bioc/GSVA.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/GSVA/ "Bioconductor devel build")
                                     +[![Bioconductor Dependencies](http://bioconductor.org/shields/dependencies/devel/GSVA.svg)](http://bioconductor.org/packages/devel/bioc/html/GSVA.html#since "Number of recursive dependencies needed to install package")
                                      The `GSVA` package allows one to perform a change in coordinate systems of molecular measurements, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods such as functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. For citing `GSVA` as a software package, please use the following reference:

@@ -25,9 +25,7 @@ need first to install the development version of R that you can find at [http://
                                      ```r
                                      install.packages("BiocManager")
                                     -BiocManager::install("BiocInstaller", version="devel")
                                     -BiocInstaller::useDevel()
                                     -BiocManager::install("GSVA")
                                     +BiocManager::install("GSVA", version = "devel")
                                      ```
                                      Alternatively, you can install it from GitHub using the [devtools](https://github.com/hadley/devtools "devtools") package.

Updated vignette and README.

Updated README.

Updated README.

Updated README.

Updated README.

Updated README.

Updated README.

Added the possibility of doing the ECDF estimation using parallel calculations.

Updated badges in README.

Updated README.

Fixed badges in README.

Fix typo in README.

clean up the use of BiocInstaller

Replacing biocLite() by BiocManager::install().

Replacing biocLite() by BiocManager::install().

Updated README.md

Updated NEWS and README.md files.

Added README file.