Commit 1bae0283 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update README formatting

parent 096fbe9c

README.Rmd

+1 −5
Original line number Diff line number Diff line
@@ -10,13 +10,9 @@ date: "`r format(Sys.time(), '%A %d %B %Y')`" 
output:

  prettydoc::html_pretty:

       theme: cayman

  #html_document:

       #theme: united

       number_sections: true

       toc: true

       toc_depth: 4

       #toc_float: true

       #code_folding: show

       keep_md: true

       keep_html: true

toc-title: "Table of Contents"
@@ -74,7 +70,7 @@ If you use this tool, please [cite](#Citation) to acknowledge the efforts of the 
new features to the maintainers with and [issue](#Issues) on GitHub. Details on how to [install](#Install) and [run](#Usage) are provided

below. Please see the [help](#Help) and [examples](#Examples) to try solve your problem before submitting an issue.



Details on the [Docker image](#Docker) are given below.

Details on the [Docker image](#Docker) are given below. We recommend using Docker unless you have a server environment with cellranger installed already.



### Supported Technologies

README.html

+2 −2
Original line number Diff line number Diff line
@@ -96,7 +96,7 @@ 
</div>



<section class="main-content">

<p><img 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<p><img 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<p><img src="data:image/svg+xml;charset=utf-8;base64,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" alt="Docker Stars" /> <img src="data:image/svg+xml;charset=utf-8;base64,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" alt="Docker Pulls" /> <img src="data:image/svg+xml;charset=utf-8;base64,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" alt="Docker Image Version (latest by date)" /></p>

<div id="universc" class="section level1">

<h1><span class="header-section-number">1</span> UniverSC</h1>
@@ -115,7 +115,7 @@ 
<h2><span class="header-section-number">1.1</span> Purpose</h2>

<p>We’ve developed a bash script that will run cellranger on FASTQ files for these technologies. See below for details on how to use it.</p>

<p>If you use this tool, please <a href="#Citation">cite</a> to acknowledge the efforts of the authors. You can report problems and request new features to the maintainers with and <a href="#Issues">issue</a> on GitHub. Details on how to <a href="#Install">install</a> and <a href="#Usage">run</a> are provided below. Please see the <a href="#Help">help</a> and <a href="#Examples">examples</a> to try solve your problem before submitting an issue.</p>

<p>Details on the <a href="#Docker">Docker image</a> are given below.</p>

<p>Details on the <a href="#Docker">Docker image</a> are given below. We recommend using Docker unless you have a server environment with cellranger installed already.</p>

<div id="supported-technologies" class="section level3">

<h3><span class="header-section-number">1.1.1</span> Supported Technologies</h3>

<p>In principle, any technology with a cell barcode and unique molecular identifier (UMI) can be supported.</p>

README.md

+1 −5
Original line number Diff line number Diff line
@@ -10,13 +10,9 @@ date: "Wednesday 08 July 2020" 
output:

  prettydoc::html_pretty:

       theme: cayman

  #html_document:

       #theme: united

       number_sections: true

       toc: true

       toc_depth: 4

       #toc_float: true

       #code_folding: show

       keep_md: true

       keep_html: true

toc-title: "Table of Contents"
@@ -74,7 +70,7 @@ If you use this tool, please [cite](#Citation) to acknowledge the efforts of the 
new features to the maintainers with and [issue](#Issues) on GitHub. Details on how to [install](#Install) and [run](#Usage) are provided

below. Please see the [help](#Help) and [examples](#Examples) to try solve your problem before submitting an issue.



Details on the [Docker image](#Docker) are given below.

Details on the [Docker image](#Docker) are given below. We recommend using Docker unless you have a server environment with cellranger installed already.



### Supported Technologies

CRA Git | Maintained and supported by SUSTech CRA and CCSE