Update author and title headers

neurogenomics · Jul 10, 2024 · fa45153 · fa45153
1 parent feeeea2
commit fa45153
Show file tree

Hide file tree

Showing 7 changed files with 44 additions and 44 deletions.
diff --git a/.github/.gitignore b/.github/.gitignore
diff --git a/.gitignore b/.gitignore
@@ -48,3 +48,4 @@ inst/markdown/test.Rmd
 .gitignore
 codecov.yml
 !.github/codecov.yml
+docs/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -88,5 +88,4 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: FALSE
 RoxygenNote: 7.3.2
-SystemRequirements: Meme Suite (v5.3.3 or above)
-    <http://meme-suite.org/doc/download.html>
+SystemRequirements: MEME Suite (v5.3.3 or above) <http://meme-suite.org/doc/download.html>
diff --git a/README.Rmd b/README.Rmd
@@ -1,12 +1,9 @@
 ---
-title: "<code>MotifPeeker</code><br>Benchmarking Epigenomic Profiling Methods Using Motif Enrichment"  
-author: "`r rworkflows::use_badges()`" 
-date: "<h4>Updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
 output:
   github_document
 ---
 
-```{r, echo=FALSE, include=FALSE}
+```{r, echo = FALSE, include = FALSE}
 pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
 title <- gsub("\n"," ",read.dcf("DESCRIPTION", fields = "Title")[1])
 description <- gsub("\n"," ",read.dcf("DESCRIPTION", fields = "Description")[1])
@@ -15,8 +12,16 @@ owner <- strsplit(URL,"/")[[1]][4]
 repo <- strsplit(URL,"/")[[1]][5]
 ```
 
+# <code>MotifPeeker</code><br>Benchmarking Epigenomic Profiling Methods Using Motif Enrichment  
+![](https://github.com/neurogenomics/MotifPeeker/raw/master/inst/hex/hex.png){style='height: 300px !important;'}
 
-# Introduction
+`r rworkflows::use_badges(add_hex = FALSE, add_authors = FALSE)`
+
+**Authors: Hiranyamaya (Hiru) Dash, Thomas Roberts, Nathan Skene**  
+**Updated:** ***`r format(Sys.Date(), '%b-%d-%Y')`***  
+
+
+## Introduction
 
 `MotifPeeker` is used to compare and analyse datasets from epigenomic
 profiling methods with motif enrichment as the key benchmark. The package
@@ -34,7 +39,7 @@ motifs.
 
 <!-- > `r utils::citation(pkg)$textVersion` -->
 
-# Installation 
+## Installation 
 
 `MotifPeeker` uses
 [`memes`](https://www.bioconductor.org/packages/release/bioc/html/memes.html)
@@ -60,14 +65,18 @@ if(!require("remotes")) install.packages("remotes")
 remotes::install_github("`r paste(owner,repo,sep='/')`")
 library(`r pkg`)
 ```
-## Documentation 
 
-### [Website](https://`r owner`.github.io/`r repo`) 
-### [Getting started](https://`r owner`.github.io/`r repo`/articles/`r pkg`) 
+
+### Documentation 
+
+#### [EpiCompare Website](https://`r owner`.github.io/`r repo`) 
+#### [Get Started](https://neurogenomics.github.io/MotifPeeker/articles/MotifPeeker.html) 
+#### [Docker/Singularity Container](https://neurogenomics.github.io/MotifPeeker/articles/docker.html) 
+
 
 <hr>
 
-## Session Info
+### Session Info
 
 <details>
 ```{r}

diff --git a/README.md b/README.md
@@ -1,7 +1,10 @@
-<code>MotifPeeker</code><br>Benchmarking Epigenomic Profiling Methods
-Using Motif Enrichment
-================
-<img src='https://github.com/neurogenomics/MotifPeeker/raw/master/inst/hex/hex.png' title='Hex sticker for MotifPeeker' height='300'><br>
+
+# <code>MotifPeeker</code><br>Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
+
+<img
+src="https://github.com/neurogenomics/MotifPeeker/raw/master/inst/hex/hex.png"
+style="height: 300px !important;" />
+
 [![License: GPL (\>=
 3)](https://img.shields.io/badge/license-GPL%20(%3E=%203)-blue.svg)](https://cran.r-project.org/web/licenses/GPL%20(%3E=%203))
 [![](https://img.shields.io/badge/devel%20version-0.99.0-black.svg)](https://github.com/neurogenomics/MotifPeeker)
@@ -11,15 +14,12 @@ Using Motif Enrichment
 status](https://github.com/neurogenomics/MotifPeeker/workflows/rworkflows/badge.svg)](https://github.com/neurogenomics/MotifPeeker/actions)
 [![](https://codecov.io/gh/neurogenomics/MotifPeeker/branch/master/graph/badge.svg)](https://app.codecov.io/gh/neurogenomics/MotifPeeker)
 <br>
-<a href='https://app.codecov.io/gh/neurogenomics/MotifPeeker/tree/master' target='_blank'><img src='https://codecov.io/gh/neurogenomics/MotifPeeker/branch/master/graphs/icicle.svg' title='Codecov icicle graph' width='200' height='50' style='vertical-align: top;'></a>  
-<h4>  
-Authors: <i>Hiranyamaya Dash, Thomas Roberts, Nathan Skene</i>  
-</h4>
-<h4>  
-Updated: <i>Jul-04-2024</i>  
-</h4>
+<a href='https://app.codecov.io/gh/neurogenomics/MotifPeeker/tree/master' target='_blank'><img src='https://codecov.io/gh/neurogenomics/MotifPeeker/branch/master/graphs/icicle.svg' title='Codecov icicle graph' width='200' height='50' style='vertical-align: top;'></a>
 
-# Introduction
+**Authors: Hiranyamaya Dash, Thomas Roberts, Nathan Skene**  
+**Updated:** ***Jul-10-2024***
+
+## Introduction
 
 `MotifPeeker` is used to compare and analyse datasets from epigenomic
 profiling methods with motif enrichment as the key benchmark. The
@@ -36,7 +36,7 @@ package outputs an HTML report consisting of three sections:
 <!-- If you use `MotifPeeker`, please cite:  -->
 <!-- >  -->
 
-# Installation
+## Installation
 
 `MotifPeeker` uses
 [`memes`](https://www.bioconductor.org/packages/release/bioc/html/memes.html)
@@ -64,15 +64,17 @@ remotes::install_github("neurogenomics/MotifPeeker")
 library(MotifPeeker)
 ```
 
-## Documentation
+### Documentation
+
+#### [EpiCompare Website](https://neurogenomics.github.io/MotifPeeker)
 
-### [Website](https://neurogenomics.github.io/MotifPeeker)
+#### [Get Started](https://neurogenomics.github.io/MotifPeeker/articles/MotifPeeker-doc.html)
 
-### [Getting started](https://neurogenomics.github.io/MotifPeeker/articles/MotifPeeker)
+#### [Docker/Singularity Container](https://neurogenomics.github.io/MotifPeeker/articles/docker.html)
 
 <hr>
 
-## Session Info
+### Session Info
 
 <details>
 

diff --git a/vignettes/templateR.Rmd → vignettes/MotifPeeker.Rmd b/vignettes/templateR.Rmd → vignettes/MotifPeeker.Rmd
@@ -1,17 +1,13 @@
 ---
 title: Get started
-author: '<h4>Authors: <i>`r auths <- eval(parse(text = gsub("person","c",
-    read.dcf("../DESCRIPTION",fields = "Authors@R"))));
-    paste(auths[names(auths)=="given"],auths[names(auths)=="family"],
-    collapse = ", ")`</i></h4>'
-date: '<h4>Vignette updated: <i>`r format( Sys.Date(), "%b-%d-%Y")`</i></h4>'
 output: rmarkdown::html_document
 vignette: |
-    %\VignetteIndexEntry{templateR}
+    %\VignetteIndexEntry{MotifPeeker}
     %\usepackage[utf8]{inputenc}
     %\VignetteEngine{knitr::rmarkdown}
 ---
 
+**Updated:** ***`r format(Sys.Date(), '%b-%d-%Y')`***  
 
 ```{r, echo=FALSE, include=FALSE}
 pkg <- read.dcf("../DESCRIPTION", fields = "Package")[1]

diff --git a/vignettes/docker.Rmd b/vignettes/docker.Rmd
@@ -1,9 +1,5 @@
 ---
 title: Docker/Singularity Containers
-author: '<h4>Authors: <i>`r auths <- eval(parse(text = gsub("person","c",read.dcf("../DESCRIPTION",
-  fields = "Authors@R"))));paste(auths[names(auths)=="given"],auths[names(auths)=="family"],
-  collapse = ", ")`</i></h4>'
-date: '<h4>Vignette updated: <i>`r format(Sys.Date(), "%b-%d-%Y")`</i></h4>'
 output:
   rmarkdown::html_document:
     md_extensions: -autolink_bare_uris
@@ -20,6 +16,8 @@ vignette: |
     %\VignetteEngine{knitr::rmarkdown}
 ---
 
+**Updated:** ***`r format(Sys.Date(), '%b-%d-%Y')`***  
+
 
 ```{r setup, include=FALSE}
 #### Package name ####
@@ -70,8 +68,6 @@ docker run \
     `r cont`
 ```  
 
-Access RStudio by visiting [http://localhost:8900/](http://localhost:8900/).
-
 ### NOTES
 
 * Make sure to replace `<your_password>` above with whatever you want your
@@ -102,8 +98,6 @@ Finally, launch the containerised Rstudio by entering the
 following URL in any web browser:
 *http://localhost:8900/*
 
-Login using the credentials set during the Installation steps.  
-
 
 # Session Info