Update links in README and vignettes

README.Rmd

@@ -16,7 +16,7 @@ knitr::opts_chunk$set(
 # JBrowseR <img src='man/figures/logo.png' align="right" height="136" />
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/elliothershberg/JBrowseR/workflows/R-CMD-check/badge.svg)](https://github.com/elliothershberg/JBrowseR/actions)
+[![R-CMD-check](https://github.com/GMOD/JBrowseR/workflows/R-CMD-check/badge.svg)](https://github.com/gmod/JBrowseR/actions)
 [![CRAN status](https://www.r-pkg.org/badges/version/JBrowseR)](https://CRAN.R-project.org/package=JBrowseR)
 <!-- badges: end -->
 
@@ -41,7 +41,7 @@ And the development version from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("devtools")
-devtools::install_github("elliothershberg/JBrowseR")
+devtools::install_github("gmod/JBrowseR")
 ```
 ## Example
 
@@ -59,7 +59,7 @@ JBrowseR("ViewHg19",
 
 In order to get started with JBrowseR, please refer to the vignette that best suits your needs:
 
-- [Introduction](https://elliothershberg.github.io/JBrowseR/articles/JBrowseR.html)
-- [Custom browser tutorial](https://elliothershberg.github.io/JBrowseR/articles/custom-browser-tutorial.html)
-- [JSON configuration tutorial](https://elliothershberg.github.io/JBrowseR/articles/json-tutorial.html)
-- [Creating URLS](https://elliothershberg.github.io/JBrowseR/articles/creating-urls.html)
+- [Introduction](https://gmod.github.io/JBrowseR/articles/JBrowseR.html)
+- [Custom browser tutorial](https://gmod.github.io/JBrowseR/articles/custom-browser-tutorial.html)
+- [JSON configuration tutorial](https://gmod.github.io/JBrowseR/articles/json-tutorial.html)
+- [Creating URLS](https://gmod.github.io/JBrowseR/articles/creating-urls.html)

README.md

@@ -5,7 +5,7 @@
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/elliothershberg/JBrowseR/workflows/R-CMD-check/badge.svg)](https://github.com/elliothershberg/JBrowseR/actions)
+[![R-CMD-check](https://github.com/GMOD/JBrowseR/workflows/R-CMD-check/badge.svg)](https://github.com/gmod/JBrowseR/actions)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/JBrowseR)](https://CRAN.R-project.org/package=JBrowseR)
 <!-- badges: end -->
@@ -36,7 +36,7 @@ And the development version from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("devtools")
-devtools::install_github("elliothershberg/JBrowseR")
+devtools::install_github("gmod/JBrowseR")
 ```
 
 ## Example
@@ -57,10 +57,10 @@ JBrowseR("ViewHg19",
 In order to get started with JBrowseR, please refer to the vignette that
 best suits your needs:
 
--   [Introduction](https://elliothershberg.github.io/JBrowseR/articles/JBrowseR.html)
+-   [Introduction](https://gmod.github.io/JBrowseR/articles/JBrowseR.html)
 -   [Custom browser
-    tutorial](https://elliothershberg.github.io/JBrowseR/articles/custom-browser-tutorial.html)
+    tutorial](https://gmod.github.io/JBrowseR/articles/custom-browser-tutorial.html)
 -   [JSON configuration
-    tutorial](https://elliothershberg.github.io/JBrowseR/articles/json-tutorial.html)
+    tutorial](https://gmod.github.io/JBrowseR/articles/json-tutorial.html)
 -   [Creating
-    URLS](https://elliothershberg.github.io/JBrowseR/articles/creating-urls.html)
+    URLS](https://gmod.github.io/JBrowseR/articles/creating-urls.html)

vignettes/JBrowseR.Rmd

@@ -73,11 +73,11 @@ While the hg19 and hg38 views can be great tools for quickly launching a browser
 The main interface of this package involves using the more general `View` component.
 For a tutorial showing how to create a small Shiny application with custom data tracks, head to:
 
-[Custom browser tutorial](https://elliothershberg.github.io/JBrowseR/articles/custom-browser-tutorial.html)
+[Custom browser tutorial](https://gmod.github.io/JBrowseR/articles/custom-browser-tutorial.html)
 
 Although the `View` components provides fairly exhaustive access to the customization options of JBrowse 2, it does not expose all of the options available.
 If you find yourself wanting to use advanced features such as coloring features with JavaScript callbacks, or to use more specific rendering functions, it is possible to use the `JsonView` to use a JSON configured browser.
 This provides full access to the configuration API available for JavaScript users of JBrowse 2.
 For a tutorial on what this looks like, visit:
 
-[JSON configuration tutorial](https://elliothershberg.github.io/JBrowseR/articles/json-tutorial.html)
+[JSON configuration tutorial](https://gmod.github.io/JBrowseR/articles/json-tutorial.html)

vignettes/custom-browser-tutorial.Rmd

@@ -51,7 +51,7 @@ For the rest of the tutorial code, we are going to use the following already hos
 - `https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz.gzi`
 
 However, these are the same steps for preparing any assembly for use with the browser.
-For notes on creating URLs for your data either locally or hosted, read more [here](https://elliothershberg.github.io/JBrowseR/articles/creating-urls.html).
+For notes on creating URLs for your data either locally or hosted, read more [here](https://gmod.github.io/JBrowseR/articles/creating-urls.html).
 
 ## Creating a minimal shiny app
 

vignettes/json-tutorial.Rmd

@@ -12,7 +12,7 @@ knitr::opts_chunk$set(eval = FALSE)
 ```
 
 The main interface of JBrowseR involves using the `View` component.
-An introduction to using this interface can be found [here](https://elliothershberg.github.io/JBrowseR/articles/custom-browser-tutorial.html).
+An introduction to using this interface can be found [here](https://gmod.github.io/JBrowseR/articles/custom-browser-tutorial.html).
 JBrowseR has several R functions for generating configuration to pass to the `View` component.
 Under the hood, these functions are returning strings of JBrowse 2 JSON configuration.