diff --git a/.Rbuildignore b/.Rbuildignore
index 4a937af91d8c3e9b47e6a1a38963b1808e27bab8..38288d10b1e5f8b7236a7cd7fc69e5ac577bc15a 100644
--- a/.Rbuildignore
+++ b/.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$
+
diff --git a/DESCRIPTION b/DESCRIPTION
index 5dbda7aef74b86882989edadd0352686e2d9a602..85c0eb2deb365cd06a491f0ab4098739c9abee96 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
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)
diff --git a/R/app_ui.R b/R/app_ui.R
index d6bae8c3837781f668721b4fc5528823b1ed674b..55898a86c94c3a14d294a372b5da72df87d3eb35 100644
--- a/R/app_ui.R
+++ b/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(
diff --git a/README.Rmd b/README.Rmd
index 687f32dd071a854e9f2437232efb9e2d20a325cb..3663724cb2c41d34d9338e778766a9d52ea09684 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -17,7 +17,10 @@ knitr::opts_chunk$set(
<!-- badges: start -->
-[](https://lifecycle.r-lib.org/articles/stages.html#experimental) [](https://joss.theoj.org/papers/e03bb9530fd2e1c0621e35352b71691e) [](https://archive.softwareheritage.org/swh:1:dir:5d122436bf50a8cac09857ef266170585a3fddc9;origin=https://forgemia.inra.fr/migale/easy16s) [](https://hal.science/hal-04304559)
+[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[](https://doi.org/10.21105/joss.06704)
+[](https://archive.softwareheritage.org/swh:1:dir:5d122436bf50a8cac09857ef266170585a3fddc9;origin=https://forgemia.inra.fr/migale/easy16s)
+[](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* : [](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
diff --git a/README.md b/README.md
index e5149d185ceb2eea59b415aa6d6cd150e45e5999..b001b9f69d8fd48204a6a379413b5edb45c8429f 100644
--- a/README.md
+++ b/README.md
@@ -6,8 +6,8 @@
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[](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)
+[](https://doi.org/10.21105/joss.06704)
[](https://archive.softwareheritage.org/swh:1:dir:5d122436bf50a8cac09857ef266170585a3fddc9;origin=https://forgemia.inra.fr/migale/easy16s)
[](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
-resourcesâ€*.
+If you use `easy16S` in your research or applications, please cite the
+associated publication in *Journal of Open Source Software* :
+[](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
diff --git a/inst/CITATION b/inst/CITATION
new file mode 100644
index 0000000000000000000000000000000000000000..5310d90b4ac7b3e6a09f3cb9d33da57531674bd1
--- /dev/null
+++ b/inst/CITATION
@@ -0,0 +1,22 @@
+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"
+)
diff --git a/inst/WORDLIST b/inst/WORDLIST
index d88f66018653debdd8d399cd914006eab8ec7cad..30d1083bd8bf1c62851ec5918299f7a1df991f0b 100644
--- a/inst/WORDLIST
+++ b/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