Merge pull request #17 from Wedge-lab/publication_update

Publication update

DESCRIPTION

@@ -1,7 +1,8 @@
 Package: AmplificationTimeR
 Type: Package
 Title: Timing of Individual Amplicitation Events in Cancer
-Version: 1.1.1
+Version: 1.1.2
+Date: 2024-06-06
 RoxygenNote: 7.2.2
 Encoding: UTF-8
 License: GPL (>= 3)

README.md

@@ -4,6 +4,8 @@
   [![R-CMD-check](https://github.com/Wedge-lab/AmplificationTimeR/actions/workflows/check-standard.yml/badge.svg)](https://github.com/Wedge-lab/AmplificationTimeR/actions/workflows/check-standard.yml)
   <!-- badges: end -->
 
+ <img src="man/AmplificationTimeR_hexagon.png" align="right" width="250" />
+
 - [AmplificationTimeR](#amplificationtimer)
   - [Citation](#citation)
   - [Introduction](#introduction)
@@ -21,7 +23,15 @@
 
 
 ## Citation
-If you use `AmplificationTimeR` in your work, please cite our manuscript (currently under review - details TBC).  
+If you use `AmplificationTimeR` in your work, please cite our manuscript:
+
+> G Maria Jakobsdottir, Stefan C Dentro, Robert G Bristow, David C Wedge, AmplificationTimeR: an R package for timing sequential amplification events, Bioinformatics, Volume 40, Issue 6, June 2024, btae281, https://doi.org/10.1093/bioinformatics/btae281
+
+A bibtex citation including package version number can be generated by running:
+```
+library(AmplificationTimeR)
+print(citation(package="AmplificationTimeR"), bibtex=TRUE)
+```
 
 ## Introduction
 `AmplificationTimeR` is an R package for timing individual amplification and whole genome duplication events affecting regions of the tumour genome that have been focally amplified.  

inst/CITATION

@@ -0,0 +1,30 @@
+year = sub("-.*","",meta$Date)
+note <- sprintf("R package version %s", meta$Version)
+
+bibentry(
+  bibtype  = "Article",
+  title    = "AmplificationTimeR: An R Package for Timing Sequential Amplification Events",
+  author   = c(person(c("G.", "Maria"), "Jakobsdottir"),
+                    person(c("Stefan", "C."), "Dentro"),
+                    person(c("Robert","G."), "Bristow"),
+                    person(c("David","C."), "Wedge")),
+  journal  = "Bioinformatics",
+  year     = "2024",
+  volume   = "40",
+  number   = "6",
+  pages    = "btae281",
+  publisher="Oxford University Press",
+  doi      = "10.1093/bioinformatics/btae281",
+  note     = note
+)
+
+bibentry(bibtype = "manual",
+  title   = "AmplificationTimeR",
+  author  = c(person(c("G.", "Maria"), "Jakobsdottir"),
+                    person(c("Stefan", "C."), "Dentro"),
+                    person(c("Robert","G."), "Bristow"),
+                    person(c("David","C."), "Wedge")),
+  year    = year,
+  note    = note,
+  url     = "https://github.com/Wedge-lab/AmplificationTimeR"
+)