tidyomics · william-hutchison · Feb 20, 2024 · Feb 1, 2024 · Feb 1, 2024 · Feb 1, 2024
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -34,9 +34,9 @@ In brief, the process to add a post is:
 
 1. Create a fork of the `tidyomicsBlog` repository.
 2. Create a new directory for your post in the format of YYYY-MM-DD-post-name, within the `tidyomicsBlog/blog/content/post` directory. 
-3. Write your blog post as an Rmd file and add it to the directory you created.
+3. Write your blog post as an Rmd file and add it to the directory you created. All files needed for your Rmd file to run should also be placed within the directory you created.
 4. Change your working directory to `tidyomicsBlog/blog`.
-4. Call the function `blogdown::build_site(build_rmd = 'newfile')` to create a html file from your Rmd file.
+4. Call the function `blogdown::build_site(build_rmd = "newfile")` to create a html file from your Rmd file.
 5. Call the function `blogdown::serve_site()` to locally render the website and inspect your work.
 6. And you're done! If it all looks good, commit your changes and create a pull request to integrate your new post into the blog.
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: tidyomicsBlog
 Title: The tidyomics blog
-Version: 1.2.0
+Version: 1.2.1
 Authors@R: c(
     person("Stefano", "Mangiola", email="[email protected]",
     role = c("aut","cre"),

diff --git a/blog/public/404.html b/blog/public/404.html
@@ -23,7 +23,7 @@
 
 
 
-<meta name="generator" content="Hugo 0.121.1 with theme even" />
+<meta name="generator" content="Hugo 0.115.4 with theme even" />
 
 
 <link rel="canonical" href="https://tidyomics.github.io/tidyomicsBlog/404.html" />
@@ -43,9 +43,9 @@
 <meta property="og:description" content="The Tidyomics Blog" />
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://tidyomics.github.io/tidyomicsBlog/404.html" />
-
 <meta itemprop="name" content="404 Page not found">
-<meta itemprop="description" content="The Tidyomics Blog"><meta name="twitter:card" content="summary"/><meta name="twitter:title" content="404 Page not found"/>
+<meta itemprop="description" content="The Tidyomics Blog"><meta name="twitter:card" content="summary"/>
+<meta name="twitter:title" content="404 Page not found"/>
 <meta name="twitter:description" content="The Tidyomics Blog"/>
 
 <!--[if lte IE 9]>
@@ -92,7 +92,7 @@
   <div class="container" id="mobile-panel">
     <header id="header" class="header">
         <div class="logo-wrapper">
-  <a href="/" class="logo">The Tidyomics Blog</a>
+  <a href=/tidyomicsBlog/ class="logo">The Tidyomics Blog</a>
 </div>
 
 
@@ -163,7 +163,7 @@ <h1 class="error-emoji"></h1>
   <span class="copyright-year">
     &copy; 
     2017 - 
-    2023<span class="heart"><i class="iconfont icon-heart"></i></span><span>Stefano Mangiola, Maria Doyle</span>
+    2024<span class="heart"><i class="iconfont icon-heart"></i></span><span>Stefano Mangiola, Maria Doyle</span>
   </span>
 </div>
 

diff --git a/blog/public/about/index.html b/blog/public/about/index.html
@@ -25,7 +25,7 @@
 
 
 
-<meta name="generator" content="Hugo 0.121.1 with theme even" />
+<meta name="generator" content="Hugo 0.115.4 with theme even" />
 
 
 <link rel="canonical" href="https://tidyomics.github.io/tidyomicsBlog/about/" />
@@ -49,14 +49,14 @@
 <meta property="og:url" content="https://tidyomics.github.io/tidyomicsBlog/about/" /><meta property="article:section" content="" />
 <meta property="article:published_time" content="2017-08-20T21:38:52+08:00" />
 <meta property="article:modified_time" content="2017-08-28T21:41:52+08:00" />
-
 <meta itemprop="name" content="About">
 <meta itemprop="description" content="Hugo is a static site engine written in Go.
 It makes use of a variety of open source projects including:
 Cobra Viper J Walter Weatherman Cast Learn more and contribute on GitHub."><meta itemprop="datePublished" content="2017-08-20T21:38:52+08:00" />
 <meta itemprop="dateModified" content="2017-08-28T21:41:52+08:00" />
 <meta itemprop="wordCount" content="32">
-<meta itemprop="keywords" content="" /><meta name="twitter:card" content="summary"/><meta name="twitter:title" content="About"/>
+<meta itemprop="keywords" content="" /><meta name="twitter:card" content="summary"/>
+<meta name="twitter:title" content="About"/>
 <meta name="twitter:description" content="Hugo is a static site engine written in Go.
 It makes use of a variety of open source projects including:
 Cobra Viper J Walter Weatherman Cast Learn more and contribute on GitHub."/>
@@ -105,7 +105,7 @@
   <div class="container" id="mobile-panel">
     <header id="header" class="header">
         <div class="logo-wrapper">
-  <a href="/" class="logo">The Tidyomics Blog</a>
+  <a href=/tidyomicsBlog/ class="logo">The Tidyomics Blog</a>
 </div>
 
 
@@ -180,7 +180,7 @@
   <span class="copyright-year">
     &copy; 
     2017 - 
-    2023<span class="heart"><i class="iconfont icon-heart"></i></span><span>Stefano Mangiola, Maria Doyle</span>
+    2024<span class="heart"><i class="iconfont icon-heart"></i></span><span>Stefano Mangiola, Maria Doyle</span>
   </span>
 </div>
 

diff --git a/blog/public/categories/all-platforms/index.html b/blog/public/categories/all-platforms/index.html
@@ -23,7 +23,7 @@
 
 
 
-<meta name="generator" content="Hugo 0.121.1 with theme even" />
+<meta name="generator" content="Hugo 0.115.4 with theme even" />
 
 
 <link rel="canonical" href="https://tidyomics.github.io/tidyomicsBlog/categories/all-platforms/" />
@@ -45,9 +45,9 @@
 <meta property="og:description" content="The Tidyomics Blog" />
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://tidyomics.github.io/tidyomicsBlog/categories/all-platforms/" />
-
 <meta itemprop="name" content="all platforms">
-<meta itemprop="description" content="The Tidyomics Blog"><meta name="twitter:card" content="summary"/><meta name="twitter:title" content="all platforms"/>
+<meta itemprop="description" content="The Tidyomics Blog"><meta name="twitter:card" content="summary"/>
+<meta name="twitter:title" content="all platforms"/>
 <meta name="twitter:description" content="The Tidyomics Blog"/>
 
 <!--[if lte IE 9]>
@@ -94,7 +94,7 @@
   <div class="container" id="mobile-panel">
     <header id="header" class="header">
         <div class="logo-wrapper">
-  <a href="/" class="logo">The Tidyomics Blog</a>
+  <a href=/tidyomicsBlog/ class="logo">The Tidyomics Blog</a>
 </div>
 
 
@@ -172,7 +172,7 @@ <h2 class="archive-name">all platforms</h2>
   <span class="copyright-year">
     &copy; 
     2017 - 
-    2023<span class="heart"><i class="iconfont icon-heart"></i></span><span>Stefano Mangiola, Maria Doyle</span>
+    2024<span class="heart"><i class="iconfont icon-heart"></i></span><span>Stefano Mangiola, Maria Doyle</span>
   </span>
 </div>
 

diff --git a/blog/public/categories/all-platforms/index.xml b/blog/public/categories/all-platforms/index.xml
@@ -6,14 +6,22 @@
     <description>Recent content in all platforms on The Tidyomics Blog</description>
     <generator>Hugo -- gohugo.io</generator>
     <language>en</language>
-    <lastBuildDate>Wed, 07 Jul 2021 00:00:00 +0000</lastBuildDate>
-    <atom:link href="https://tidyomics.github.io/tidyomicsBlog/categories/all-platforms/index.xml" rel="self" type="application/rss+xml" />
+    <lastBuildDate>Wed, 07 Jul 2021 00:00:00 +0000</lastBuildDate><atom:link href="https://tidyomics.github.io/tidyomicsBlog/categories/all-platforms/index.xml" rel="self" type="application/rss+xml" />
     <item>
       <title>Tidy-transcriptomics manifesto</title>
       <link>https://tidyomics.github.io/tidyomicsBlog/post/2021-07-07-tidy-transcriptomics-manifesto/</link>
       <pubDate>Wed, 07 Jul 2021 00:00:00 +0000</pubDate>
+
       <guid>https://tidyomics.github.io/tidyomicsBlog/post/2021-07-07-tidy-transcriptomics-manifesto/</guid>
-      <description>&#xA;&lt;script src=&#34;{{&lt; blogdown/postref &gt;}}index.en_files/header-attrs/header-attrs.js&#34;&gt;&lt;/script&gt;&#xA;&#xA;&lt;div id=&#34;TOC&#34;&gt;&#xA;&#xA;&lt;/div&gt;&#xA;&#xA;</description>
+      <description>
+&lt;script src=&#34;{{&lt; blogdown/postref &gt;}}index.en_files/header-attrs/header-attrs.js&#34;&gt;&lt;/script&gt;
+
+&lt;div id=&#34;TOC&#34;&gt;
+
+&lt;/div&gt;
+
+</description>
     </item>
+
   </channel>
 </rss>
diff --git a/blog/public/categories/index.html b/blog/public/categories/index.html
@@ -23,7 +23,7 @@
 
 
 
-<meta name="generator" content="Hugo 0.121.1 with theme even" />
+<meta name="generator" content="Hugo 0.115.4 with theme even" />
 
 
 <link rel="canonical" href="https://tidyomics.github.io/tidyomicsBlog/categories/" />
@@ -45,9 +45,9 @@
 <meta property="og:description" content="The Tidyomics Blog" />
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://tidyomics.github.io/tidyomicsBlog/categories/" />
-
 <meta itemprop="name" content="Categories">
-<meta itemprop="description" content="The Tidyomics Blog"><meta name="twitter:card" content="summary"/><meta name="twitter:title" content="Categories"/>
+<meta itemprop="description" content="The Tidyomics Blog"><meta name="twitter:card" content="summary"/>
+<meta name="twitter:title" content="Categories"/>
 <meta name="twitter:description" content="The Tidyomics Blog"/>
 
 <!--[if lte IE 9]>
@@ -94,7 +94,7 @@
   <div class="container" id="mobile-panel">
     <header id="header" class="header">
         <div class="logo-wrapper">
-  <a href="/" class="logo">The Tidyomics Blog</a>
+  <a href=/tidyomicsBlog/ class="logo">The Tidyomics Blog</a>
 </div>
 
 
@@ -162,7 +162,7 @@
   <span class="copyright-year">
     &copy; 
     2017 - 
-    2023<span class="heart"><i class="iconfont icon-heart"></i></span><span>Stefano Mangiola, Maria Doyle</span>
+    2024<span class="heart"><i class="iconfont icon-heart"></i></span><span>Stefano Mangiola, Maria Doyle</span>
   </span>
 </div>
 

diff --git a/blog/public/categories/index.xml b/blog/public/categories/index.xml
@@ -6,14 +6,15 @@
     <description>Recent content in Categories on The Tidyomics Blog</description>
     <generator>Hugo -- gohugo.io</generator>
     <language>en</language>
-    <lastBuildDate>Wed, 07 Jul 2021 00:00:00 +0000</lastBuildDate>
-    <atom:link href="https://tidyomics.github.io/tidyomicsBlog/categories/index.xml" rel="self" type="application/rss+xml" />
+    <lastBuildDate>Wed, 07 Jul 2021 00:00:00 +0000</lastBuildDate><atom:link href="https://tidyomics.github.io/tidyomicsBlog/categories/index.xml" rel="self" type="application/rss+xml" />
     <item>
       <title>all platforms</title>
       <link>https://tidyomics.github.io/tidyomicsBlog/categories/all-platforms/</link>
       <pubDate>Wed, 07 Jul 2021 00:00:00 +0000</pubDate>
+
       <guid>https://tidyomics.github.io/tidyomicsBlog/categories/all-platforms/</guid>
       <description></description>
     </item>
+
   </channel>
 </rss>
diff --git a/blog/public/index.html b/blog/public/index.html
@@ -23,7 +23,7 @@
 
 
 
-<meta name="generator" content="Hugo 0.121.1 with theme even" />
+<meta name="generator" content="Hugo 0.115.4 with theme even" />
 
 
 <link rel="canonical" href="https://tidyomics.github.io/tidyomicsBlog/" />
@@ -45,9 +45,9 @@
 <meta property="og:description" content="The Tidyomics Blog" />
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://tidyomics.github.io/tidyomicsBlog/" />
-
 <meta itemprop="name" content="The Tidyomics Blog">
-<meta itemprop="description" content="The Tidyomics Blog"><meta name="twitter:card" content="summary"/><meta name="twitter:title" content="The Tidyomics Blog"/>
+<meta itemprop="description" content="The Tidyomics Blog"><meta name="twitter:card" content="summary"/>
+<meta name="twitter:title" content="The Tidyomics Blog"/>
 <meta name="twitter:description" content="The Tidyomics Blog"/>
 
 <!--[if lte IE 9]>
@@ -94,7 +94,7 @@
   <div class="container" id="mobile-panel">
     <header id="header" class="header">
         <div class="logo-wrapper">
-  <a href="/" class="logo">The Tidyomics Blog</a>
+  <a href=/tidyomicsBlog/ class="logo">The Tidyomics Blog</a>
 </div>
 
 
@@ -206,7 +206,7 @@ <h1 class="post-title"><a class="post-link" href="/tidyomicsBlog/post/2021-07-07
   <span class="copyright-year">
     &copy; 
     2017 - 
-    2023<span class="heart"><i class="iconfont icon-heart"></i></span><span>Stefano Mangiola, Maria Doyle</span>
+    2024<span class="heart"><i class="iconfont icon-heart"></i></span><span>Stefano Mangiola, Maria Doyle</span>
   </span>
 </div>
 

diff --git a/blog/public/index.xml b/blog/public/index.xml
@@ -6,28 +6,43 @@
     <description>Recent content on The Tidyomics Blog</description>
     <generator>Hugo -- gohugo.io</generator>
     <language>en</language>
-    <lastBuildDate>Thu, 07 Dec 2023 00:00:00 +0000</lastBuildDate>
-    <atom:link href="https://tidyomics.github.io/tidyomicsBlog/index.xml" rel="self" type="application/rss+xml" />
+    <lastBuildDate>Thu, 07 Dec 2023 00:00:00 +0000</lastBuildDate><atom:link href="https://tidyomics.github.io/tidyomicsBlog/index.xml" rel="self" type="application/rss+xml" />
     <item>
       <title>About</title>
       <link>https://tidyomics.github.io/tidyomicsBlog/about/</link>
       <pubDate>Sun, 20 Aug 2017 21:38:52 +0800</pubDate>
+
       <guid>https://tidyomics.github.io/tidyomicsBlog/about/</guid>
-      <description>Hugo is a static site engine written in Go.&#xA;It makes use of a variety of open source projects including:&#xA;Cobra Viper J Walter Weatherman Cast Learn more and contribute on GitHub.</description>
+      <description>Hugo is a static site engine written in Go.
+It makes use of a variety of open source projects including:
+Cobra Viper J Walter Weatherman Cast Learn more and contribute on GitHub.</description>
     </item>
+
     <item>
       <title>The new tidy sccomp interface</title>
       <link>https://tidyomics.github.io/tidyomicsBlog/post/2023-12-07-tidy-sccomp/</link>
       <pubDate>Thu, 07 Dec 2023 00:00:00 +0000</pubDate>
+
       <guid>https://tidyomics.github.io/tidyomicsBlog/post/2023-12-07-tidy-sccomp/</guid>
-      <description>We announce the new tidy and modular interface for a sccomp, which improves modularity, and clarity. The main change is the modularisation of sccomp in functions which can be linked with the pipe operator |&amp;gt;.&#xA;Function Description Estimation: sccomp_stimate() which is usually run once in the analysis (per model). Testing: sccomp_test() which candy run multiple times, depending on how many contrasts you want to test (e.g. age, untreated vs treated).</description>
+      <description>We announce the new tidy and modular interface for a sccomp, which improves modularity, and clarity. The main change is the modularisation of sccomp in functions which can be linked with the pipe operator |&amp;gt;.
+Function Description Estimation: sccomp_stimate() which is usually run once in the analysis (per model). Testing: sccomp_test() which candy run multiple times, depending on how many contrasts you want to test (e.g. age, untreated vs treated).</description>
     </item>
+
     <item>
       <title>Tidy-transcriptomics manifesto</title>
       <link>https://tidyomics.github.io/tidyomicsBlog/post/2021-07-07-tidy-transcriptomics-manifesto/</link>
       <pubDate>Wed, 07 Jul 2021 00:00:00 +0000</pubDate>
+
       <guid>https://tidyomics.github.io/tidyomicsBlog/post/2021-07-07-tidy-transcriptomics-manifesto/</guid>
-      <description>&#xA;&lt;script src=&#34;{{&lt; blogdown/postref &gt;}}index.en_files/header-attrs/header-attrs.js&#34;&gt;&lt;/script&gt;&#xA;&#xA;&lt;div id=&#34;TOC&#34;&gt;&#xA;&#xA;&lt;/div&gt;&#xA;&#xA;</description>
+      <description>
+&lt;script src=&#34;{{&lt; blogdown/postref &gt;}}index.en_files/header-attrs/header-attrs.js&#34;&gt;&lt;/script&gt;
+
+&lt;div id=&#34;TOC&#34;&gt;
+
+&lt;/div&gt;
+
+</description>
     </item>
+
   </channel>
 </rss>
diff --git a/blog/public/post/2021-07-07-tidy-transcriptomics-manifesto/index.html b/blog/public/post/2021-07-07-tidy-transcriptomics-manifesto/index.html
@@ -23,7 +23,7 @@
 
 
 
-<meta name="generator" content="Hugo 0.121.1 with theme even" />
+<meta name="generator" content="Hugo 0.115.4 with theme even" />
 
 
 <link rel="canonical" href="https://tidyomics.github.io/tidyomicsBlog/post/2021-07-07-tidy-transcriptomics-manifesto/" />
@@ -52,7 +52,6 @@
 <meta property="og:url" content="https://tidyomics.github.io/tidyomicsBlog/post/2021-07-07-tidy-transcriptomics-manifesto/" /><meta property="article:section" content="post" />
 <meta property="article:published_time" content="2021-07-07T00:00:00+00:00" />
 <meta property="article:modified_time" content="2021-07-07T14:16:36+10:00" />
-
 <meta itemprop="name" content="Tidy-transcriptomics manifesto">
 <meta itemprop="description" content="
 
@@ -64,7 +63,8 @@
 "><meta itemprop="datePublished" content="2021-07-07T00:00:00+00:00" />
 <meta itemprop="dateModified" content="2021-07-07T14:16:36+10:00" />
 <meta itemprop="wordCount" content="2913">
-<meta itemprop="keywords" content="tidyomics/tidyomicsBlog,manifesto,transcriptomics,tidyverse," /><meta name="twitter:card" content="summary"/><meta name="twitter:title" content="Tidy-transcriptomics manifesto"/>
+<meta itemprop="keywords" content="tidyomics/tidyomicsBlog,manifesto,transcriptomics,tidyverse," /><meta name="twitter:card" content="summary"/>
+<meta name="twitter:title" content="Tidy-transcriptomics manifesto"/>
 <meta name="twitter:description" content="
 
 
@@ -118,7 +118,7 @@
   <div class="container" id="mobile-panel">
     <header id="header" class="header">
         <div class="logo-wrapper">
-  <a href="/" class="logo">The Tidyomics Blog</a>
+  <a href=/tidyomicsBlog/ class="logo">The Tidyomics Blog</a>
 </div>
 
 
@@ -667,7 +667,7 @@ <h3>tidySummarizedExperiment and tidySingleCellEXeperiment</h3>
   <span class="copyright-year">
     &copy; 
     2017 - 
-    2023<span class="heart"><i class="iconfont icon-heart"></i></span><span>Stefano Mangiola, Maria Doyle</span>
+    2024<span class="heart"><i class="iconfont icon-heart"></i></span><span>Stefano Mangiola, Maria Doyle</span>
   </span>
 </div>
 

diff --git a/blog/public/post/2023-12-07-tidy-sccomp/index.Rmd b/blog/public/post/2023-12-07-tidy-sccomp/index.Rmd
@@ -12,8 +12,6 @@ vignette: >
   %\usepackage[UTF-8]{inputenc}
 ---
 
-We announce the new tidy and modular interface for a `sccomp`, which improves modularity, and clarity. The main change is the modularisation of `sccomp` in functions which can be linked with the pipe operator `|>`.
-
 <!-- badges: start -->
 
 [![Lifecycle:maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) [![R build status](https://github.com/stemangiola/sccomp/actions/workflows/rworkflows.yml/badge.svg)](https://github.com/stemangiola/tidyseurat/actions/)
@@ -22,6 +20,7 @@ We announce the new tidy and modular interface for a `sccomp`, which improves mo
 
 ![](https://raw.githubusercontent.com/stemangiola/sccomp/master/inst/logo-01.png){width="120px"}
 
+We announce the new tidy and modular interface for a `sccomp`, which improves modularity, and clarity. The main change is the modularisation of `sccomp` in functions which can be linked with the pipe operator `|>`.
 
 
 ```{r echo=FALSE, message=FALSE, warning=FALSE}
@@ -146,6 +145,4 @@ outlier_free_estimate |>
 
 ```
 
-```{r}
-sessionInfo()
-```
+