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<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<!-- -->
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="application/xml+xhtml; charset=UTF-8" />
<title>enclone (bit.ly/enclone)</title>
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<! –– 💩 💩 💩 🔴 🔨 🔨 🔨 🔨 🔨 🔨 🔴 💩 💩 💩 PUT DOWN YOUR HAMMER. THIS IS AN AUTO-GENERATED FILE. PLEASE DO NOT EDIT
IT. THANK YOU FOR YOUR COOPERATION, SINCERELY, THE BENEVOLENT OVERLORDS 💩 💩 💩 🔴 🔨 🔨 🔨 🔨 🔨 🔨 🔴 💩 💩 💩
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<body>
<br>
<a href="#help">
<img src="img/enclone_banner.png" alt="enclone banner" title="enclone banner" width=100% />
</a>
<header>
<h1><b><span style="color:rgb(120,123,175);font-weight:900">enclone</span></b> (beta)</h1>
<h3>Accurate and user-friendly computational tool for clonal grouping to study the adaptive immune system
<h3>
<h4>(Antigen analysis is not supported)</h4>
</header>
<p><b><a href="https://10xgenomics.com/">10x Genomics</a></b> Chromium Single Cell V(D)J data
containing B cell
receptor (BCR) and T cell receptor (TCR) RNA sequences are entered as input data to
<span style="color:rgb(120,123,175);font-weight:900">enclone</span>. Based on the
input, <span style="color:rgb(120,123,175);font-weight:900">enclone</span> finds and organizes cells
arising from the same progenitors into groups
(clonotypes) and
compactly displays each clonotype along with its salient features, including mutated amino
acids.
</p>
<p style="border: 2px; border-style: solid; border-color: black; background-color: #EBF4FC;
padding: 8px; font-size: 110%">
<span style="color:rgb(120,123,175);font-weight:900">enclone</span> (beta) is provided as a tool for use
by the community to accelerate immunology research.
<span style="color:rgb(120,123,175);font-weight:900">enclone</span> is only supported via
<a href="mailto:enclone@10xgenomics.com"><span
style="color:rgb(120,123,175);font-weight:900">enclone</span>@10xgenomics.com</a>.
The clonotype assignment algorithm that is part of <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> is integrated into Cell Ranger.
</p>
<p><span style="color:rgb(120,123,175);font-weight:900">enclone</span> has been designed for immunologists but
anyone can download and experiment with it.</p>
<p><b>Background:</b> when you get sick, your body mounts an immune response by selectively
amplifying immune cells and mutations within these selected cells. <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> allows you to see the
history of
single immune cells within a biological sample (such as a blood draw or biopsy). This history
reflects how the cognate receptors of these cells evolved in response to antigens, including
viruses, bacteria, and tumors.</p>
<table rules="all" cellpadding="3" style="border: 1px solid black">
<tbody>
<tr>
<td align="left"><a href="#intro"> 1. Introduction </a></td>
<td align="left"><a href="#help"> 8. Help </a></td>
</tr>
<tr>
<td align="left"><a href="#objective"> 2. Objective </a></td>
<td align="left"><a href="#output"> 9. Understanding <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> output </a>
</td>
</tr>
<tr>
<td align="left"><a href="#why"> 3. Why <span
style="color:rgb(120,123,175);font-weight:900">enclone</span>? </a></td>
<td align="left"><a href="#multiomic"> 10. Combining multiomic data </a></td>
</tr>
<tr>
<td align="left"><a href="#inputs"> 4. Data input </a></td>
<td align="left"><a href="#honeycomb"> 11. Visualizing multiple clonotypes at
once </a></td>
</tr>
<tr>
<td align="left"><a href="#software"> 5. Software </a></td>
<td align="left"><a href="#powerunlimitedpower"> 12. The power of <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> </a></td>
</tr>
<tr>
<td align="left"><a href="#download"> 6. Installing <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> </a></td>
<td align="left"><a href="#questions"> 13. Questions </a></td>
</tr>
<tr>
<td align="left"><a href="#running"> 7. Running <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> </a></td>
<td align="left"><a href="#whereami"> 14. Where am I? </a></td>
</tr>
</tbody>
</table>
<br>
<hr>
<p><a name="intro" style="display:block; position:relative; top:-20px;"></a></p>
<h2>Introduction</h2>
<p>The body defends itself from antigens, like viruses, bacteria, and tumors, by recognizing the
antigens and mounting an immune response through selective amplification of immune cells and
mutations within selected cells. <span style="color:rgb(120,123,175);font-weight:900">enclone</span>
enables profiling of the history of single immune
cells within a biological sample (such as a blood draw or a biopsy) by mapping the evolution of the
cognate BCRs and TCRs of those cells responding to antigen exposure. This history reflects how the
cognate receptors of these cells evolved in response to various antigens.</p>
<p><a name="objective" style="display:block; position:relative; top:-20px;"></a></p>
<h2>Objective</h2>
<p>Using <span style="color:rgb(120,123,175);font-weight:900">enclone</span> to profile B and T cell receptors
for any sample using Chromium Single Cell
V(D)J as input enables you to make the best use of your data. You can explore the biology of these
cells without help from a computational expert!</p>
<p>The objective of <span style="color:rgb(120,123,175);font-weight:900">enclone</span> is to:</p>
<table style="width:100%; margin-top: -25px; margin-bottom: -25px">
<tr>
<th>
<p style="text-align: left; font-weight:normal; border: 2px; border-style: solid;
padding: 8px; font-size: 130%; line-height:130%">
<span style="color:red">Find</span> and <span style="color:red">display</span> clonotypes:
groups of T and B cells sharing the same fully rearranged common ancestor.
</p>
</th>
<th style="padding-left: 20px; text-align: left; font-weight:normal">
<p style="margin-bottom:5px"><span style="color:red">Find:</span>
It is easy to mistakenly put unrelated cells in
the same clonotype, or "pollute" a clonotype with extraneous chains.
<b><span style="color:rgb(120,123,175);font-weight:900">enclone</span>'s algorithms make
<i>finding</i> accurate.</b>
</p>
<p style="margin-top:5px"><span style="color:red">Display:</span>
It is challenging to compactly represent a
large repertoire of data. <b><span
style="color:rgb(120,123,175);font-weight:900">enclone</span> enables compact,
easy-to-grasp data
<i>display</i>.</b></p>
</th>
</tr>
</table>
<p>The diversity of BCR and TCR chains, containing various combinations of V, D, and/or J segments,
broadens the immune repertoire to protect against a wide variety of pathogens. The figure below
illustrates the concept of a <em>BCR clonotype</em>. A similar concept applies to TCRs but without
somatic hypermutations.</p>
<!-- TODO: update from Tech Comm (Keri) -->
<img src="img/what_is_a_clonotype.svg" alt="what is a clonotype" title="what is a clonotype"
style="max-width:80%;"></a>
<p>Each cell in a clonotype is typically represented by two or three chains, and this information is
present and directly observable in single cell V(D)J data. <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> computationally approximates
the clonotypes
from the data with high accuracy (see below). The methods of <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> are described
<a href="pages/auto/help.how.html">briefly in the online documentation for <span
style="color:rgb(120,123,175);font-weight:900">enclone</span></a>, and see
below.
</p>
<hr>
<p><a name="why" style="display:block; position:relative; top:-20px;"></a></p>
<h2>Why use <span style="color:rgb(120,123,175);font-weight:900">enclone</span>?</h2>
<p>
<b><span style="color:rgb(120,123,175);font-weight:900">enclone</span></b> has unique features!
</p>
<p>
<b>Unique insights into 10x Genomics data</b>: <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> has been designed and tested
extensively to
gain in-depth insight and perspective regarding 10x Genomics single cell V(D)J datasets. Other
similar tools
may be used, but frequently, <span style="color:rgb(120,123,175);font-weight:900">enclone</span> will
provide a different answer, which in turn may affect
the biological interpretation of the data.
</p>
<p>
<b>Speed</b>: <span style="color:rgb(120,123,175);font-weight:900">enclone</span> is very fast, allowing
analysis of datasets in seconds.
</p>
<p>
<b>Easy installation</b>: The software is <a href="#download">easy to install</a> and to use.
</p>
<hr>
<p><a name="inputs" style="display:block; position:relative; top:-20px;"></a></p>
<h2>Inputs to <span style="color:rgb(120,123,175);font-weight:900">enclone</span></h2>
<p>10x Genomics single cell 5' data<sup>†</sup></p>
<p><sup>†</sup><i>
BCR or TCR RNA sequences generated using the <a href="https://www.10xgenomics.com">10x Genomics</a>
Chromium Single Cell Immune Profiling Solution and Cell Ranger 3.1 or higher are the inputs to
<span style="color:rgb(120,123,175);font-weight:900">enclone</span>. <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> can also process and display gene
expression and Feature Barcode data
from the same cells. The latter can be used to quantify cell surface proteins, antigen binding,
CRISPR
sgRNA, and other cellular features. You can see a list of publications that use 10x VDJ data
<a
href="https://www.10xgenomics.com/resources/publications?sortBy=publications-relevance&refinementList%5BproductGroups%5D%5B0%5D=Single%20Cell%20Immune%20Profiling&page=1">here</a>.
</i>
</p>
<hr>
<p><a name="software" style="display:block; position:relative; top:-20px;"></a></p>
<h2>The <span style="color:rgb(120,123,175);font-weight:900">enclone</span> software</h2>
<p><span style="color:rgb(120,123,175);font-weight:900">enclone</span> is beta software<sup>††</sup> released
under <a href="LICENSE.txt">this license</a>.
Binary executables for Linux and Mac and Windows can be directly downloaded from this page, as can
sample 10x Genomics datasets.
<span style="color:rgb(120,123,175);font-weight:900">enclone</span> can be run on a laptop, desktop, or
server.
</p>
<p>
To use <span style="color:rgb(120,123,175);font-weight:900">enclone</span>, basic knowledge of the
command line is necessary. The command line is easy to
learn, and a
colleague may be able to help you if you are unfamiliar. Additional skills, like programming,
are not required. The command line can be dynamically changed to select specific clonotypes and
fields you wish to
see. <span style="color:rgb(120,123,175);font-weight:900">enclone</span> is fast, typically responding in
seconds (if run on a single dataset).
</p>
<p>
<span style="color:rgb(120,123,175);font-weight:900">enclone</span>, in addition to <a
href="https://support.10xgenomics.com/single-cell-vdj">Cell Ranger and
Loupe</a>
(and in which the core algorithm of <span style="color:rgb(120,123,175);font-weight:900">enclone</span>
will be integrated at a later point in time),
supports the
analysis of V(D)J and other data from the
<a href="https://www.10xgenomics.com/products/single-cell-immune-profiling/">Chromium Single Cell Immune
Profiling
solution</a>.
</p>
<p>
<sup>††</sup><i>beta software implies that it is still being actively developed, with
features being added/modified,
and on rare occasions may involve breaking syntax that previously worked. See
<a href="pages/auto/history.html">this page</a> for the history of changes.</i>
</p>
<hr>
<p><a name="download" style="display:block; position:relative; top:-20px;"></a></p>
<h2>Installing <span style="color:rgb(120,123,175);font-weight:900">enclone</span></h2>
<p>
You can run <span style="color:rgb(120,123,175);font-weight:900">enclone</span> directly from a
<b>Linux</b> or <b>Mac</b> terminal window; see
<a href="pages/auto/windows.html">here</a> for <b>Windows</b> instructions.
</p>
<table>
<tr>
<th align=left style="font-weight: normal">Type this </th>
<th align=left style="padding: 3px; font-weight: normal; border: 2px solid black">
<pre
style="margin-top:3px; margin-bottom:3px"><code>curl -sSf -L bit.ly/enclone_install | bash -s <span style="color:red; font-weight: bold">SIZE</span></code></pre>
</th>
<th align=left style="font-weight: normal">
where <code style="color:red; font-weight: bold">SIZE</code> is
<code>small</code>, <code>medium</code>, <code>large</code>, or <code>colossus</code>,
according to:
</th>
</tr>
</table>
<br>
<table rules="all" cellpadding="3" style="border: 2px solid black">
<tr>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
<code>small</code>
</p>
</th>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
load small dataset collection (one dataset, 123085)
</p>
</th>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
30 MB
</p>
</th>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
do this if your internet connection is very slow
</p>
</th>
</tr>
<tr>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
<code>medium</code>
</p>
</th>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
load medium dataset collection
</p>
</th>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
3400 MB
</p>
</th>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
do this for a moderate number of datasets (~120)
</p>
</th>
</tr>
<tr>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
<code>large</code>
</p>
</th>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
load large dataset collection
</p>
</th>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
4700 MB
</p>
</th>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
do this for a large number of datasets (~240)
</p>
</th>
</tr>
<tr>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
<code>colossus</code>
</p>
</th>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
load colossus dataset collection
</p>
</th>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
26400 MB
</p>
</th>
<th align=left style="font-weight: normal; border: 2px solid black">
<p style="margin: 4px">
same as large but includes gene expression data for many datasets
</p>
</th>
</tr>
</table>
<p>The command does three things:</p>
<ol>
<li>Puts the <span style="color:rgb(120,123,175);font-weight:900">enclone</span> executable (for Linux or
Mac as appropriate) in <code>~/bin</code>.</li>
<li>If needed, adds a line to your bash initialization file so that <code>~/bin</code> is included.
</li>
<li>Puts <span style="color:rgb(120,123,175);font-weight:900">enclone</span> datasets in
<code>~/enclone</code>.</li>
</ol>
Additional details can be found <a href="pages/auto/installation_details.html">here</a>.
Restart your terminal session; you can now run <span
style="color:rgb(120,123,175);font-weight:900">enclone</span>.</p>
<table>
<tr>
<th align=left style="padding: 3px; font-weight: normal; border: 2px solid black">
Please see
<a href="pages/auto/install_issues.html">here</a> if you have an installation problem.
</th>
</tr>
</table>
<p><span style="color:red; font-weight:bold">To update, type the same command!</span>
<span style="font-weight:bold">
You can also type <code>enclone UPDATE</code>, which does the same thing (except for older versions
of <span style="color:rgb(120,123,175);font-weight:900">enclone</span>). Only required files will be
downloaded.
See <a href="pages/auto/history.html">history</a> for the history of changes to
<span style="color:rgb(120,123,175);font-weight:900">enclone</span>.
</span>
</p>
<p>Information about previous releases of <span style="color:rgb(120,123,175);font-weight:900">enclone</span>,
matching particular Cell Ranger releases is
<a href="pages/auto/cellranger.html">here</a>, along with an inventory of <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> changes that
affect Cell Ranger output.
</p>
<table>
<tr>
<th align=left style="padding: 3px; font-weight: normal; border: 2px solid black">
On a Mac, the Terminal application can enter weird states. One behavior is an intermittently
spinning disk. Another is that some executables (perhaps <span
style="color:rgb(120,123,175);font-weight:900">enclone</span>) may respond with
<code>Command not found</code> or <code>Permission denied</code>. In such cases, it may work
to close the Terminal application (<code>Quit Terminal</code> on the top bar), then reopen it.
This should only be needed rarely, if at all.
</th>
</tr>
</table>
<hr>
<p><a name="running" style="display:block; position:relative; top:-20px;"></a></p>
<h2>Running <span style="color:rgb(120,123,175);font-weight:900">enclone</span></h2>
<p>Running <span style="color:rgb(120,123,175);font-weight:900">enclone</span> can be as simple as typing e.g.
</p>
<pre><code>enclone BCR=/home/my_name/experiment_123
</code></pre>
<p>where the path is where your Cell Ranger outputs live, but there are many options to learn
about. For example, if you want to combine many datasets, you can do that, but you probably
need to provide a metadata file that describes the datasets. You can find most of the <span
style="color:rgb(120,123,175);font-weight:900">enclone</span>
documentation within its online menus. To get started you should:</p>
<ol>
<li>
<p>Type <code>enclone help</code>, to make sure your terminal window works for
<span style="color:rgb(120,123,175);font-weight:900">enclone</span>.
</p>
<p style="border: 2px; border-style: solid; border-color: black; padding: 8px; width: 630px">
<b>A few things you need to know:</b>
<br><b>1.</b> To view the online help, your terminal window needs to be 100 characters wide
(or wider).
<br><b>2.</b> When you view <span style="color:rgb(120,123,175);font-weight:900">enclone</span>
output, you will in general need to make your window even
wider.
<br><b>3.</b> How wide depends on the data and the fields you choose to show.
<br><b>4. If it's not wide enough, the output will "wrap" and be very confusing!</b>
<br><b>5.</b> Having clonotype tables in a Terminal on a Mac can make the Terminal less
responsive. This may depend on the operating system version.
</p>
</li>
<li>
<p>Type <code>enclone</code> to get to the main <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> help menu.</p>
</li>
</ol>
<hr>
<p><a name="help" style="display:block; position:relative; top:-20px;"></a></p>
<h2>Help</h2>
<p
style="border: 2px; border-style: solid; border-color: black; padding: 8px; width: 530px; margin-left: 3px">
<b>From any page, clicking on the banner at the top will take you back
<span style="color:red">here</span>.</b>
</p>
<table>
<tr valign="top">
<td>
<table rules="all" cellpadding="3" style="border: 2px solid black; margin-right: 8px">
<tbody>
<tr>
<td colspan="2" style="text-align:center; background-color: #BBF9ED"><b>pages on
site and accessible from command line</b></td>
</tr>
<tr>
<td align="left"><b>command</b></td>
<td align="left"><b>what it provides</b></td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.setup.html">enclone help</a></td>
<td align="left">help to test for correct setup</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.main.html">enclone</a></td>
<td align="left">what you see here; guide to all the docs</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.quick.html">enclone help quick</a>
</td>
<td align="left">quick guide to getting started</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.how.html">enclone help how</a></td>
<td align="left">outline of how <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> works,
see also heuristics</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.command.html">enclone help command</a>
</td>
<td align="left">info about <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> command
line processing</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.glossary.html">enclone help
glossary</a></td>
<td align="left">glossary of terms used by <span
style="color:rgb(120,123,175);font-weight:900">enclone</span>,
conventions</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.example1.html">enclone help
example1</a></td>
<td align="left">explanation of an example</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.example2.html">enclone help
example2</a></td>
<td align="left">example of gene expression, feature barcodes</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.input.html">enclone help input</a>
</td>
<td align="left">how to provide input to <span
style="color:rgb(120,123,175);font-weight:900">enclone</span></td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.input_tech.html">enclone help
input_tech</a></td>
<td align="left">how to provide input to <span
style="color:rgb(120,123,175);font-weight:900">enclone</span>
(technical notes)</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.parseable.html">enclone help
parseable</a></td>
<td align="left">parseable output</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.filter.html">enclone help filter</a>
</td>
<td align="left">clonotype filtering, feature enrichment scanning</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.special.html">enclone help special</a>
</td>
<td align="left">special filtering options</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.lvars.html">enclone help lvars</a>
</td>
<td align="left">lead column options</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.cvars.html">enclone help cvars</a>
</td>
<td align="left">per chain column options</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.amino.html">enclone help amino</a>
</td>
<td align="left">per chain column options for amino acids</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.display.html">enclone help display</a>
</td>
<td align="left">other clonotype display options</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.indels.html">enclone help indels</a>
</td>
<td align="left">insertion and deletion handling</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.color.html">enclone help color</a>
</td>
<td align="left">how <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> uses
color, and related things</td>
<tr>
<td align="left"><a href="pages/auto/help.faq.html">enclone help faq</a></td>
<td align="left">frequently asked questions</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/help.all.html">enclone help all</a></td>
<td align="left">concatenation of all the help pages <br> (USE THIS TO SEARCH
ALL HELP PAGES)</td>
</tr>
</tbody>
</table>
</td>
<td>
<table rules="all" cellpadding="3" style="border: 2px solid black">
<tbody>
<tr>
<td colspan="2" style="text-align:center; background-color: #BBF9ED"><b>other
pages on site</b></td>
</tr>
<tr>
<td align="left"><b>page</b></td>
<td align="left"><b>audience</b></td>
</tr>
<tr>
<td align="left"><a href="pages/auto/history.html">history of changes</a></td>
<td align="left">everyone</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/expanded.html">detecting illusory
clonotypes</a></td>
<td align="left">everyone</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/dev.html">enclone developers guide</a></td>
<td align="left">people who want to contribute code</td>
</tr>
<tr>
<td align="left"><a href="LICENSE.txt">license</a></td>
<td align="left">everyone</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/windows.html">Windows</a></td>
<td align="left">people using Windows computers</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/heuristics.html">notes on heuristics</a>
</td>
<td align="left">those curious about the algorithm</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/default_filters.html"><span
style="color:rgb(120,123,175);font-weight:900">enclone</span>
default filtering</a></td>
<td align="left">those curious about the algorithm</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/plot.html">plots</a></td>
<td align="left">everyone</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/tree.html">making phylogenetic trees</a>
</td>
<td align="left">everyone</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/install_issues.html">installation
troubleshooting
</a></td>
<td align="left">if you have trouble installing</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/installation_details.html">installation
details
</a></td>
<td align="left">those curious what install command does</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/innate.html">iNKT and MAIT cells
</a></td>
<td align="left">those curious about iNKT and MAIT cells</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/features.html">V(D)J features
</a></td>
<td align="left">those curious about CDR*, etc. calculations</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/variables.html">enclone variable inventory
</a></td>
<td align="left">everyone</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/d_genes.html">D genes, junction regions
</a></td>
<td align="left">everyone</td>
</tr>
<tr>
<td align="left"><a href="pages/auto/cellranger.html"><span
style="color:rgb(120,123,175);font-weight:900">enclone</span> in
cellranger
</a></td>
<td align="left">everyone</td>
</tr>
</tbody>
</table>
<p>
<table>
<tr>
<th align=left style="padding: 3px; font-weight: normal; border: 3px solid red">
Additional information may be found in our bioRxiv preprint
<br>
<a href="https://www.biorxiv.org/content/10.1101/2022.04.21.489084v1.full.pdf">
enclone: precision clonotyping and analysis of immune receptors</a>.
</th>
</tr>
</table>
</p>
<p>And we're here to help! See the bottom of this page for how to contact us.</p>
</tr>
</table>
<br>
<hr>
<p><a name="output" style="display:block; position:relative; top:-20px;"></a></p>
<h2>Understanding <span style="color:rgb(120,123,175);font-weight:900">enclone</span> output</h2>
<p>The example below shows how <span style="color:rgb(120,123,175);font-weight:900">enclone</span> displays
clonotypes. Understanding this display is
important for using <span style="color:rgb(120,123,175);font-weight:900">enclone</span>. Consult the
available <span style="color:rgb(120,123,175);font-weight:900">enclone</span> documentation and use
the sample datasets to understand <span style="color:rgb(120,123,175);font-weight:900">enclone</span>
features and output.</p>
<img src="img/enclone_annotated_example.svg" alt="enclone annotated example" title="enclone annotated example"
style="max-width:100%;"></a>
<b>Notice the compression in two directions</b>:
<ol>
<li><b>Vertically</b> to group cells into a single line if they have identical V(D)J
transcripts
(instead of showing one line for every cell).</li>
<li><b>Horizontally</b>, a flexible concept, to show by default all positions exhibiting a
difference from the reference and all positions in the CDR3 (instead of showing
all transcript positions, only "interesting" positions are shown).</li>
</ol>
<p>Approximately the same output would be obtained by typing:</p>
<pre><code>enclone BCR=123085 CDR3=CTRDRDLRGATDAFDIW
</code></pre>
(As we change the algorithm, results are perturbed, and we have not updated the
diagram each time. All other outputs shown on this site are kept current.)
<p>The directory <code>123085</code> is in the directory <code>~/enclone/datasets</code> and
contains some files from a Cell Ranger run, obtained from a human ovarian cancer sample.</p>
<p style="border: 2px; border-style: solid; border-color: black; padding: 8px; width: 950px">
<b>How does <span style="color:rgb(120,123,175);font-weight:900">enclone</span> find my data?</b>
It uses a <i>search path</i> called <code>PRE</code> that is preset to
<code>~/enclone/datasets,~/enclone/datasets2</code>, and which can be set to any value, either
by setting <code>PRE=...</code> on the command line, or by setting the environment variable
<code>ENCLONE_PRE</code>. To find your data, <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> prepends <code>PRE</code> to the value
of
<code>BCR</code> or <code>TCR</code> given on the command line.
For example, all of the following argument combinations do the same thing:
<br>1. <code>BCR=123085</code> (using the default value of <code>PRE</code>)
<br>2. <code>PRE=~/enclone/datasets BCR=123085</code>
<br>3. <code>PRE=~/enclone BCR=datasets/123085</code>
<br>4. <code>BCR=~/enclone/datasets/123085</code>.
<br>There is also an argument <code>META</code> that is convenient for specifying multiple
datasets. See <a href="pages/auto/help.input.html">here</a> for how.
<br>
<br>
Please note that while paths can have non-Latin characters, best practice is to <b>not have
blanks, tabs, etc. in path names</b>. <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> can be made to work with such
characters by double
quoting the paths, but it makes things harder, and other programs you might use may break.
</p>
<p>The argument <code>CDR3=CTRDRDLRGATDAFDIW</code> causes <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> to display only clonotypes in
which
the given CDR3 sequence occurs. Many other filters are provided. In the absence of filters, all
clonotypes are shown. Clonotypes are shown from largest to smallest, and the output is
automatically paged, so you can scroll through it.</p>
<p>By default, <span style="color:rgb(120,123,175);font-weight:900">enclone</span> prints clonotypes in this
human-readable form. You can also instruct
<span style="color:rgb(120,123,175);font-weight:900">enclone</span>
to print clonotypes in machine-readable forms that are suitable for input to other programs.
</p>
<hr>
<p><a name="multiomic" style="display:block; position:relative; top:-20px;"></a></p>
<h2>Combining multiomic data</h2>
<p>Gene expression and Feature Barcode data can be displayed simultaneously alongside VDJ data. For
example, here we add columns for the same clonotype, showing the median number of UMIs detected
for all genes, and a particular gene:</p>
<pre style='font-family: "DejaVuSansMono"; line-height: 110%'><span style="font-size: 14px"><span style="color:#4c7aff;font-weight:bold;">[1] GROUP = 1 CLONOTYPES = 51 CELLS</span>
[1.1] CLONOTYPE = 51 CELLS
┌──────────────────────────┬──────────────────────────────────────┬───────────────────────────────┐
│ │ <span style="font-weight:bold;">CHAIN 1</span> │ CHAIN 2 │
│ │ <span style="font-weight:bold;">144.1.2|IGHV3-49 ◆ 53|IGHJ3</span> │ 279|IGKV3-11 ◆ 217|IGKJ5 │
│ ├──────────────────────────────────────┼───────────────────────────────┤
│ │ 1 11111111111111111 1 │ 1111111111111 │
│ │ 51 11112222222222333 4 │ 6 0001111111111 │
│ │ 53 67890123456789012 1 │ 4 7890123456789 │
│ │ ═══════CDR3══════ │ ═════CDR3════ │
│reference │ <span style="color:#72c0ff;font-weight:bold;">V</span><span style="color:#f37721;font-weight:bold;">V</span> ◦◦◦◦◦◦◦◦◦◦◦◦◦◦◦◦<span style="color:#f37721;font-weight:bold;">W</span> <span style="color:#f37721;font-weight:bold;">S</span> │ <span style="color:#f37721;font-weight:bold;">R</span> <span style="color:#e7bd20;">C</span><span style="color:#3e7dd1;font-weight:bold;">QQ</span>◦◦◦◦◦◦◦◦◦◦ │
│donor ref │ <span style="color:#f37721;font-weight:bold;">FV</span> ◦◦◦◦◦◦◦◦◦◦◦◦◦◦◦◦<span style="color:#f37721;font-weight:bold;">W</span> <span style="color:#f37721;font-weight:bold;">S</span> │ <span style="color:#f37721;font-weight:bold;">R</span> <span style="color:#e7bd20;">C</span><span style="color:#3e7dd1;font-weight:bold;">QQ</span>◦◦◦◦◦◦◦◦◦◦ │
├──────────────────────────┼──────────────────────────────────────┼───────────────────────────────┤
│<span style="font-weight:bold;"># n gex IGHV3-49_g </span>│<span style="font-weight:bold;"> .x ................. x u const </span>│<span style="font-weight:bold;"> x .x........... u const</span>│
│1 46 13385 324 │ <span style="color:#f37721;font-weight:bold;">FV</span> <span style="color:#e7bd20;">C</span><span style="color:#eb99c2;font-weight:bold;">T</span><span style="color:#e7bd20;">R</span><span style="color:#31c39a;">DR</span><span style="color:#3e7dd1;font-weight:bold;">D</span><span style="color:#31c39a;">L</span><span style="color:#f37721;font-weight:bold;">R</span><span style="color:#eb99c2;font-weight:bold;">GA</span><span style="color:#e7bd20;">T</span><span style="color:#3e7dd1;font-weight:bold;">D</span><span style="color:#72c0ff;font-weight:bold;">A</span><span style="color:#3e7dd1;font-weight:bold;">F</span><span style="color:#31c39a;">D</span><span style="color:#eb99c2;font-weight:bold;">I</span><span style="color:#f37721;font-weight:bold;">W</span> <span style="color:#f37721;font-weight:bold;">S</span> 101 IGHG1 │ <span style="color:#f37721;font-weight:bold;">R</span> <span style="color:#e7bd20;">C</span><span style="color:#3e7dd1;font-weight:bold;">QQ</span><span style="color:#72c0ff;font-weight:bold;">R</span><span style="color:#3e7dd1;font-weight:bold;">S</span><span style="color:#f37721;font-weight:bold;">NW</span><span style="color:#3e7dd1;font-weight:bold;">PP</span><span style="color:#72c0ff;font-weight:bold;">S</span><span style="color:#eb99c2;font-weight:bold;">I</span><span style="color:#e7bd20;">T</span><span style="color:#f37721;font-weight:bold;">F</span> 3769 IGKC │
│2 3 9303 544 │ <span style="color:#f37721;font-weight:bold;">F</span><span style="color:#31c39a;">M</span> <span style="color:#e7bd20;">C</span><span style="color:#eb99c2;font-weight:bold;">T</span><span style="color:#e7bd20;">R</span><span style="color:#31c39a;">DR</span><span style="color:#3e7dd1;font-weight:bold;">D</span><span style="color:#31c39a;">L</span><span style="color:#f37721;font-weight:bold;">R</span><span style="color:#eb99c2;font-weight:bold;">GA</span><span style="color:#e7bd20;">T</span><span style="color:#3e7dd1;font-weight:bold;">D</span><span style="color:#72c0ff;font-weight:bold;">A</span><span style="color:#3e7dd1;font-weight:bold;">F</span><span style="color:#31c39a;">D</span><span style="color:#eb99c2;font-weight:bold;">I</span><span style="color:#f37721;font-weight:bold;">W</span> <span style="color:#f37721;font-weight:bold;">S</span> 73 IGHG1 │ <span style="color:#f37721;font-weight:bold;">R</span> <span style="color:#e7bd20;">CH</span><span style="color:#3e7dd1;font-weight:bold;">Q</span><span style="color:#72c0ff;font-weight:bold;">R</span><span style="color:#3e7dd1;font-weight:bold;">S</span><span style="color:#f37721;font-weight:bold;">NW</span><span style="color:#3e7dd1;font-weight:bold;">PP</span><span style="color:#72c0ff;font-weight:bold;">S</span><span style="color:#eb99c2;font-weight:bold;">I</span><span style="color:#e7bd20;">T</span><span style="color:#f37721;font-weight:bold;">F</span> 7548 IGKC │
│3 1 15986 1528 │ <span style="color:#f37721;font-weight:bold;">FV</span> <span style="color:#e7bd20;">C</span><span style="color:#eb99c2;font-weight:bold;">T</span><span style="color:#e7bd20;">R</span><span style="color:#31c39a;">DR</span><span style="color:#3e7dd1;font-weight:bold;">D</span><span style="color:#31c39a;">L</span><span style="color:#f37721;font-weight:bold;">R</span><span style="color:#eb99c2;font-weight:bold;">GA</span><span style="color:#e7bd20;">T</span><span style="color:#3e7dd1;font-weight:bold;">D</span><span style="color:#72c0ff;font-weight:bold;">A</span><span style="color:#3e7dd1;font-weight:bold;">F</span><span style="color:#31c39a;">D</span><span style="color:#eb99c2;font-weight:bold;">I</span><span style="color:#f37721;font-weight:bold;">W</span> <span style="color:#f37721;font-weight:bold;">S</span> 279 IGHG1 │ <span style="color:#3e7dd1;font-weight:bold;">S</span> <span style="color:#e7bd20;">C</span><span style="color:#3e7dd1;font-weight:bold;">QQ</span><span style="color:#72c0ff;font-weight:bold;">R</span><span style="color:#3e7dd1;font-weight:bold;">S</span><span style="color:#f37721;font-weight:bold;">NW</span><span style="color:#3e7dd1;font-weight:bold;">PP</span><span style="color:#72c0ff;font-weight:bold;">S</span><span style="color:#eb99c2;font-weight:bold;">I</span><span style="color:#e7bd20;">T</span><span style="color:#f37721;font-weight:bold;">F</span> 12446 IGKC │
│4 1 1548 11 │ <span style="color:#f37721;font-weight:bold;">FV</span> <span style="color:#e7bd20;">C</span><span style="color:#eb99c2;font-weight:bold;">T</span><span style="color:#e7bd20;">R</span><span style="color:#31c39a;">DR</span><span style="color:#3e7dd1;font-weight:bold;">D</span><span style="color:#31c39a;">L</span><span style="color:#f37721;font-weight:bold;">R</span><span style="color:#eb99c2;font-weight:bold;">GA</span><span style="color:#e7bd20;">T</span><span style="color:#3e7dd1;font-weight:bold;">D</span><span style="color:#72c0ff;font-weight:bold;">A</span><span style="color:#3e7dd1;font-weight:bold;">F</span><span style="color:#31c39a;">D</span><span style="color:#eb99c2;font-weight:bold;">I</span><span style="color:#f37721;font-weight:bold;">W</span> <span style="color:#31c39a;">S</span> 33 IGHG1 │ <span style="color:#f37721;font-weight:bold;">R</span> <span style="color:#e7bd20;">C</span><span style="color:#3e7dd1;font-weight:bold;">QQ</span><span style="color:#72c0ff;font-weight:bold;">R</span><span style="color:#3e7dd1;font-weight:bold;">S</span><span style="color:#f37721;font-weight:bold;">NW</span><span style="color:#3e7dd1;font-weight:bold;">PP</span><span style="color:#72c0ff;font-weight:bold;">S</span><span style="color:#eb99c2;font-weight:bold;">I</span><span style="color:#e7bd20;">T</span><span style="color:#f37721;font-weight:bold;">F</span> 116 IGKC │
└──────────────────────────┴──────────────────────────────────────┴───────────────────────────────┘
</span></pre>
<p>To obtain this, we added the extra arguments
<code>GEX=123217 LVARSP=gex,IGHV3-49_g</code>
to the previous command. The <code>GEX</code> part points to the directory containing gene
expression data. The <code>LVARSP</code> part defines the additional columns
to be displayed.
</p>
<p>Other types of data can be brought in via Feature Barcoding / Feature Barcode Technology.
For example, the response to multiple antigens can be measured using approaches such as those
mentioned in the <a href="https://www.ncbi.nlm.nih.gov/pubmed/31787378" rel="nofollow">LIBRA-seq</a>
and <a href="https://www.researchsquare.com/article/rs-80476/v1" rel="nofollow">Wilson/Stamper/Dugan et
al.</a>
papers. These data can be displayed as additional columns.</p>
<hr>
<p><a name="honeycomb" style="display:block; position:relative; top:-20px;"></a></p>
<h2>Visualizing multiple clonotypes</h2>
<table style="width:100%">
<tr>
<th>
<img src="img/clono.svg" alt="honeycomb plot" title="honeycomb plot">
</th>
<th></th>
<th></th>
<th style="text-align: left; font-weight:normal">
<p>After selecting multiple clonotypes in <span
style="color:rgb(120,123,175);font-weight:900">enclone</span>, you can display them
using
a "honeycomb" plot.</p>
<p>In this instance, pre- and post-vaccination samples were collected from four individuals,
many datasets were generated for each sample, and these were combined in a single call
to <span style="color:rgb(120,123,175);font-weight:900">enclone</span>. Clonotypes
containing at least ten cells are shown.
The plot was generated by adding</p>
<pre><code>MIN_CELLS=10 PLOT="clono.svg,pre->blue,post->red</code>
<code>LEGEND=blue,"pre-vaccination cell",</code>
<code> red,"post-vaccination cell"</code></pre>
<p>to the <span style="color:rgb(120,123,175);font-weight:900">enclone</span> command line,
yielding the image shown here as the file
<code>clono.svg</code>.
</p>
<p>For more information about honeycomb plots,
see <a href="pages/auto/plot.html">here</a>.</p>
</th>
</tr>
</table>
<br>
<hr>
<p><a name="powerunlimitedpower" style="display:block; position:relative; top:-20px;"></a></p>
<h2>The power of <span style="color:rgb(120,123,175);font-weight:900">enclone</span></h2>
<p>There are many ways to use 10x Genomics data to study immunobiology.</p>
<p><b>Response to an antigen or vaccine</b>: <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> is a great tool for studying responses
to a
vaccine. For example, in the previous section, the red clonotypes may represent responses to
antigens in the vaccine.</p>
<p><b>Vaccine and therapeutic antibody development</b>: For certain infectious agents <i>e.g.</i> COVID-19,
a vaccine does not currently exist; different approaches may be employed in pursuit of this goal. One
such
approach is to <b>identify patient and survivor B cell clonotypes that expand in response to the
infectious
disease.</b> These define antibodies that can be used to design passive or active vaccines.</p>
<p>Additional power is added by mapping antigen specificity to multiple antigens directly via Feature
Barcode Technology (one example of this is the <a href="https://www.ncbi.nlm.nih.gov/pubmed/31787378"
rel="nofollow">LIBRA-seq</a>
publication). These data are easy to display in <span
style="color:rgb(120,123,175);font-weight:900">enclone</span>. Candidates can be selected directly
for vaccine or therapeutic
development by picking large clonotypes with high antigen counts and single or multiple antigen
specificities.</p>
<p>We are actively working on further functionality that will make this process even more effective.</p>
<p>See <a href="pages/auto/tree.html">this vignette</a> to learn how to generate phylogenetic trees using
<span style="color:rgb(120,123,175);font-weight:900">enclone</span>.
<p>Another example use of <span style="color:rgb(120,123,175);font-weight:900">enclone</span> is the <b><a
href="pages/auto/expanded.html">detection of
illusory clonotypes</a></b>.</p>
<hr>
<p><a name="questions" style="display:block; position:relative; top:-20px;"></a></p>
<h2>Questions</h2>
<p>
Please contact us with your questions and comments! We look forward to hearing your feedback and ideas to
further evolve <span style="color:rgb(120,123,175);font-weight:900">enclone</span>.
</p>
<p>
Our address is <a href="mailto:enclone@10xgenomics.com"><span
style="color:rgb(120,123,175);font-weight:900">enclone</span>@10xgenomics.com</a>.
</p>
<p>
To send us <span style="color:rgb(120,123,175);font-weight:900">enclone</span> output, please simply
<b>cut and paste text</b>, rather than send a
screenshot, except when necessary. Please send <b>both the command you used and the output</b>.
</p>
<p style="border: 2px; border-style: solid; border-color: black; background-color: #EBF4FC;
padding: 8px; font-size: 110%">
<span style="color:rgb(120,123,175);font-weight:900">enclone</span> is provided as a tool for use by the
community.
<span style="color:rgb(120,123,175);font-weight:900">enclone</span> is beta software and thus a work in
progress. We are actively making many changes and may
be unable to respond promptly to your particular request.
</p>
<hr>
<p><a name="whereami" style="display:block; position:relative; top:-20px;"></a></p>
<h2>Where am I?</h2>
<!-- dunno why negative left margin needed to line things up on left: -->
<p style="margin-left: -1.5px; margin-top: 30px; font-family: DejaVuSansMono; font-size: 200%; color: blue">
bit.ly/<span style="color:rgb(120,123,175);font-weight:900">enclone</span></p>
</body>
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