From 2833e6b5209318d25eb01b71d63bff416cad1640 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Thu, 25 Apr 2024 22:08:15 +0200
Subject: [PATCH 1/5] Add citation

---
 README.md     | 11 +++++++++++
 inst/CITATION | 11 +++++++++++
 2 files changed, 22 insertions(+)
 create mode 100644 inst/CITATION

diff --git a/README.md b/README.md
index 37fa0a1..b49574f 100644
--- a/README.md
+++ b/README.md
@@ -17,6 +17,17 @@ remotes::install_github("johrpan/geposan")
 See [this page](https://remotes.r-lib.org/reference/install_git.html) for more
 information on this command.
 
+## Publication
+
+This method and its implementation have been peer-reviewed and published in
+NAR Genomics and Bioinformatics. If you use the package in your research or
+would like to refer to our methodology, please cite the following paper:
+
+Elias F Projahn, Georg Fuellen, Michael Walter, Steffen Möller, Proposing
+candidate genes under telomeric control based on cross-species position data,
+NAR Genomics and Bioinformatics, Volume 6, Issue 2, June 2024, lqae037,
+https://doi.org/10.1093/nargab/lqae037
+
 ## Graphical interface
 
 Please also take a look at the interactive graphical web interface for geposan
diff --git a/inst/CITATION b/inst/CITATION
new file mode 100644
index 0000000..17d6334
--- /dev/null
+++ b/inst/CITATION
@@ -0,0 +1,11 @@
+bibentry(
+  bibtype = "Article",
+  title = "Proposing candidate genes under telomeric control based on cross-species position data",
+  author = "Elias F Projahn, Georg Fuellen, Michael Walter, Steffen Möller",
+  journal = "NAR Genomics and Bioinformatics",
+  year = 2024,
+  volume = 6,
+  number = 2,
+  pages = "lqae037",
+  doi = "10.1093/nargab/lqae037"
+)

From 0eb36fa59273f5e55a95957849a5f1ea5f42f054 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Thu, 25 Apr 2024 22:08:27 +0200
Subject: [PATCH 2/5] Version 1.0.1

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d8bcd23..dcba0fc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: geposan
 Title: Gene Position Analysis
-Version: 1.0.0
+Version: 1.0.1
 Authors@R:
     person(
         "Elias",

From e4d1d6203a2df6c50c9510ff9125464cf1ef08a7 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Fri, 26 Apr 2024 19:02:08 +0200
Subject: [PATCH 3/5] Correct optional dependencies

---
 DESCRIPTION | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index dcba0fc..f95f8b3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -28,9 +28,7 @@ Imports:
     rlang,
     progress
 Suggests:
-    biomaRt,
-    httr,
     plotly,
     rlog,
-    stringr,
+    RMariaDB,
     usethis

From d584cfe12dd3adc5576bd1a53ed4ebe1bf302ee7 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Sun, 23 Feb 2025 16:03:47 +0100
Subject: [PATCH 4/5] plots: Use grey background in scores_by_position

---
 R/plots.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/plots.R b/R/plots.R
index 706a4ed..7971c10 100644
--- a/R/plots.R
+++ b/R/plots.R
@@ -718,8 +718,9 @@ plot_scores_by_position <- function(ranking,
         "Percentile: {round(percentile * 100, digits = 2)}%"
       ),
       marker = list(
-        color = base_color(),
-        size = 5
+        size = 3,
+        color = "#919191",
+        opacity = 0.5
       ),
       hoverinfo = "text"
     ) |>

From fdf89e849698d83a98207f6f24ebaba1f6f8a486 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Sun, 23 Feb 2025 16:04:44 +0100
Subject: [PATCH 5/5] Version 1.1.0

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f95f8b3..038dbfe 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: geposan
 Title: Gene Position Analysis
-Version: 1.0.1
+Version: 1.1.0
 Authors@R:
     person(
         "Elias",