JOSS paper DOI

.Rbuildignore

@@ -10,6 +10,7 @@ $run_dev.*
 ^LICENSE\.md$
 ^README\.Rmd$
 ^CODE_OF_CONDUCT\.md$
+^CONTRIBUTING\.md$
 ^Dockerfile$
 ^\.dockerignore$
 ^\.gitlab-ci\.yml$
@@ -17,4 +18,7 @@ $run_dev.*
 ^check$
 ^docs$
 ^JOSS$
+^pkgdown$
 ^_pkgdown.yml$
+^CITATION.cff$
+

DESCRIPTION

 Package: easy16S
 Title: a user-friendly Shiny web-service for exploration and visualization
     of microbiome
-Version: 0.0.0.9000
+Version: 24.07
 Authors@R: c(
     person("Cédric", "Midoux", , "cedric.midoux@inrae.fr", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-7964-0929")),
@@ -11,7 +11,8 @@ Authors@R: c(
 Description: This shiny application provides users with an interactive and
     easy-to-use microbiome analysis framework.
 License: AGPL (>= 3)
-URL: https://easy16s.migale.inrae.fr
+URL: https://easy16s.migale.inrae.fr, 
+doi: 10.21105/joss.06704
 BugReports: https://forgemia.inra.fr/migale/easy16s/-/issues
 Depends:
     R (>= 4.1)

R/app_ui.R

@@ -21,7 +21,7 @@ app_ui <- function(request) {
         title = div("Easy16S", img(src = "www/favicon.png", height = "22px", style = "vertical-align:sub")),
         tags$li(class = "dropdown", tags$a(icon("readme"), headerText = "README", href = "http://easy16s.migale.inrae.fr", target = "_blank")),
         tags$li(class = "dropdown", tags$a(icon("gitlab"), headerText = "GitLab", href = "https://forgemia.inra.fr/migale/easy16s", target = "_blank")),
-        tags$li(class = "dropdown", tags$a(icon("quote-right"), headerText = "Cite Us", href = "https://easy16s.migale.inrae.fr/authors.html#citation", target = "_blank")),
+        tags$li(class = "dropdown", tags$a(list(icon("quote-right"), span("New!", class = "label label-danger")), headerText = "Cite Us", href = "https://doi.org/10.21105/joss.06704", target = "_blank")),
         mod_plot_dim_ui("plot_dim")
       ),
       dashboardSidebar(

README.Rmd

@@ -17,7 +17,10 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 
-[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![JOSS](https://joss.theoj.org/papers/e03bb9530fd2e1c0621e35352b71691e/status.svg)](https://joss.theoj.org/papers/e03bb9530fd2e1c0621e35352b71691e) [![SWH](https://archive.softwareheritage.org/badge/swh:1:dir:5d122436bf50a8cac09857ef266170585a3fddc9/)](https://archive.softwareheritage.org/swh:1:dir:5d122436bf50a8cac09857ef266170585a3fddc9;origin=https://forgemia.inra.fr/migale/easy16s) [![HAL](https://img.shields.io/badge/-hal--04304559-1E198E?style=flat&logo=HAL)](https://hal.science/hal-04304559)
+[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) 
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.06704/status.svg)](https://doi.org/10.21105/joss.06704)
+[![SWH](https://archive.softwareheritage.org/badge/swh:1:dir:5d122436bf50a8cac09857ef266170585a3fddc9/)](https://archive.softwareheritage.org/swh:1:dir:5d122436bf50a8cac09857ef266170585a3fddc9;origin=https://forgemia.inra.fr/migale/easy16s)
+[![HAL](https://img.shields.io/badge/-hal--04304559-1E198E?style=flat&logo=HAL)](https://hal.science/hal-04304559)
 
 <!-- badges: end -->
 
@@ -75,7 +78,7 @@ We have incorporated several default settings and guardrails to guide users and
 
 ## FAQ
 
-> It is called easy"16S". Can I use it with another marker? 
+> It is called easy"16S". Can I use it with another marker?
 
 Yes! Easy16S is the historical name. This tool was originally developed for 16S amplicon data. This is why the "16S" has remained in the name. It can also be used to analyze other metagenomics data such as ITS or MAGs. However, care must be taken with the interpretations made, and results must not be over-interpreted.
 
@@ -85,9 +88,30 @@ If you encounter any bugs or have suggestions for improvement, please use the [i
 
 ## Cite us
 
-We appreciate acknowledgment from research teams using Easy16S. Please include the following sentence in the publications of your analyses: *"We are grateful to the INRAE MIGALE bioinformatics facility (MIGALE, INRAE, 2020. Migale bioinformatics Facility, doi: 10.15454/1.5572390655343293E12) for providing help and computing resources"*.
+If you use `easy16S` in your research or applications, please cite the associated publication in *Journal of Open Source Software* : [![DOI](https://joss.theoj.org/papers/10.21105/joss.06704/status.svg)](https://doi.org/10.21105/joss.06704).
+
+> Midoux et al., (2024). Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data. Journal of Open Source Software, 9(103), 6704, <https://doi.org/10.21105/joss.06704>
+
+``` bibtex
+@article{easy16S,
+  title = {Easy16S: a user-friendly Shiny web-service for exploration and
+  visualization of microbiome data.},
+  author = {Cédric Midoux and Olivier Rué and Olivier Chapleur and Ariane Bize and Valentin Loux and Mahendra Mariadassou},
+  journal = {Journal of Open Source Software},
+  publisher = {The Open Journal},
+  year = {2024},
+  volume = {9},
+  number = {103},
+  pages = {6704},
+  doi = {10.21105/joss.06704},
+  issn = {2475-9066},
+  url = {https://easy16s.migale.inrae.fr},
+}
+```
+
+If you used the online version, we also appreciate acknowledgment from research teams using computing resources. Please include the following sentence in the publications of your analyses:
 
-A scientific publication related to Easy16S is currently in preparation.
+> We are grateful to the INRAE MIGALE bioinformatics facility (MIGALE, INRAE, 2020. Migale bioinformatics Facility, doi: 10.15454/1.5572390655343293E12) for providing help and computing resources.
 
 ## Code of Conduct
 

README.md

@@ -6,8 +6,8 @@
 <!-- badges: start -->
 
 [![Lifecycle:
-experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[![JOSS](https://joss.theoj.org/papers/e03bb9530fd2e1c0621e35352b71691e/status.svg)](https://joss.theoj.org/papers/e03bb9530fd2e1c0621e35352b71691e)
+stable](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.06704/status.svg)](https://doi.org/10.21105/joss.06704)
 [![SWH](https://archive.softwareheritage.org/badge/swh:1:dir:5d122436bf50a8cac09857ef266170585a3fddc9/)](https://archive.softwareheritage.org/swh:1:dir:5d122436bf50a8cac09857ef266170585a3fddc9;origin=https://forgemia.inra.fr/migale/easy16s)
 [![HAL](https://img.shields.io/badge/-hal--04304559-1E198E?style=flat&logo=HAL)](https://hal.science/hal-04304559)
 
@@ -105,14 +105,39 @@ tracker](https://forgemia.inra.fr/migale/easy16s/-/issues).
 
 ## Cite us
 
-We appreciate acknowledgment from research teams using Easy16S. Please
-include the following sentence in the publications of your analyses:
-*“We are grateful to the INRAE MIGALE bioinformatics facility (MIGALE,
-INRAE, 2020. Migale bioinformatics Facility, doi:
-10.15454/1.5572390655343293E12) for providing help and computing
-resources”*.
+If you use `easy16S` in your research or applications, please cite the
+associated publication in *Journal of Open Source Software* :
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.06704/status.svg)](https://doi.org/10.21105/joss.06704).
+
+> Midoux et al., (2024). Easy16S: a user-friendly Shiny web-service for
+> exploration and visualization of microbiome data. Journal of Open
+> Source Software, 9(103), 6704, <https://doi.org/10.21105/joss.06704>
+
+``` bibtex
+@article{easy16S,
+  title = {Easy16S: a user-friendly Shiny web-service for exploration and
+  visualization of microbiome data.},
+  author = {Cédric Midoux and Olivier Rué and Olivier Chapleur and Ariane Bize and Valentin Loux and Mahendra Mariadassou},
+  journal = {Journal of Open Source Software},
+  publisher = {The Open Journal},
+  year = {2024},
+  volume = {9},
+  number = {103},
+  pages = {6704},
+  doi = {10.21105/joss.06704},
+  issn = {2475-9066},
+  url = {https://easy16s.migale.inrae.fr},
+}
+```
+
+If you used the online version, we also appreciate acknowledgment from
+research teams using computing resources. Please include the following
+sentence in the publications of your analyses:
 
-A scientific publication related to Easy16S is currently in preparation.
+> We are grateful to the INRAE MIGALE bioinformatics facility (MIGALE,
+> INRAE, 2020. Migale bioinformatics Facility, doi:
+> 10.15454/1.5572390655343293E12) for providing help and computing
+> resources.
 
 ## Code of Conduct
 

inst/CITATION

+bibentry(
+  bibtype = "Article",
+  key = "easy16S",
+  title = "Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data.",
+  author = c(
+    person("Cédric", "Midoux", , role = c("cre", "aut"), comment = c(ORCID = "0000-0002-7964-0929")),
+    person("Olivier", "Rué", , , comment = c(ORCID = "0000-0001-7517-4724")),
+    person("Olivier", "Chapleur", , , comment = c(ORCID = "0000-0001-9460-921X")),
+    person("Ariane", "Bize", , , comment = c(ORCID = "0000-0003-4023-8665")),
+    person("Valentin", "Loux", , , comment = c(ORCID = "0000-0002-8268-915X")),
+    person("Mahendra", "Mariadassou", , role = "ctb", comment = c(ORCID = "0000-0003-2986-354X"))
+  ),
+  year = 2024,
+  journal = "Journal of Open Source Software",
+  publisher = "The Open Journal",
+  volume = 9,
+  number = 103,
+  pages = 6704,
+  doi = "10.21105/joss.06704",
+  issn = "2475-9066",
+  url = "https://easy16s.migale.inrae.fr"
+)

inst/WORDLIST

@@ -24,6 +24,7 @@ RData
 SWH
 ShinyProxy
 addin
+al
 amplicon
 bioinformaticians
 bioinformatics
@@ -34,6 +35,7 @@ compositional
 dispersions
 doi
 esquisse
+et
 ggplot
 golem
 gusta