From efb36bc938da7a5f395a40d7555d843a39adbc6c Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inrae.fr>
Date: Mon, 18 Nov 2024 12:56:04 +0100
Subject: [PATCH] JOSS paper DOI
---
.Rbuildignore | 4 ++++
DESCRIPTION | 5 +++--
R/app_ui.R | 2 +-
README.Rmd | 32 ++++++++++++++++++++++++++++----
README.md | 43 ++++++++++++++++++++++++++++++++++---------
inst/CITATION | 22 ++++++++++++++++++++++
inst/WORDLIST | 2 ++
7 files changed, 94 insertions(+), 16 deletions(-)
create mode 100644 inst/CITATION
diff --git a/.Rbuildignore b/.Rbuildignore
index 4a937af..38288d1 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 5dbda7a..85c0eb2 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 d6bae8c..55898a8 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 687f32d..3663724 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 e5149d1..b001b9f 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 0000000..5310d90
--- /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 d88f660..30d1083 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
--
GitLab