-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.html
115 lines (94 loc) · 7.71 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
<title>Deep mutational scanning (DMS) pipeline for a viral entry protein (VEP) — Deep mutational scanning (DMS) pipeline for a viral entry protein (VEP) documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="_static/alabaster.css" />
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/sphinx_highlight.js"></script>
<script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Analyze PacBio CCSs" href="analyze_pacbio_ccs.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
<div class="document">
<div class="documentwrapper">
<div class="body" role="main">
<section id="deep-mutational-scanning-dms-pipeline-for-a-viral-entry-protein-vep">
<h1>Deep mutational scanning (DMS) pipeline for a viral entry protein (VEP)<a class="headerlink" href="#deep-mutational-scanning-dms-pipeline-for-a-viral-entry-protein-vep" title="Permalink to this heading">¶</a></h1>
<p>This page documents the data analysis.
For the actual code, see <a class="reference external" href="https://github.com/dms-vep/dms-vep-pipeline">https://github.com/dms-vep/dms-vep-pipeline</a></p>
<p>Study by Jesse Bloom.</p>
<section id="analysis-notebooks">
<h2>Analysis notebooks<a class="headerlink" href="#analysis-notebooks" title="Permalink to this heading">¶</a></h2>
<p>Many of the plots in these notebooks are interactive, so try mousing over points for
details, using dropdowns, etc.</p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="analyze_pacbio_ccs.html">Analyze PacBio CCSs</a></li>
<li class="toctree-l1"><a class="reference internal" href="build_pacbio_consensus.html">Build PacBio consensus sequences</a></li>
<li class="toctree-l1"><a class="reference internal" href="build_codon_variants.html">Build the codon variants</a></li>
<li class="toctree-l1"><a class="reference internal" href="analyze_func_scores.html">Functional scores of variants for viral entry</a></li>
<li class="toctree-l1"><a class="reference internal" href="fit_globalepistasis.html">Fit global epistasis models</a></li>
<li class="toctree-l1"><a class="reference internal" href="avg_muteffects.html">Functional effects of mutations across replicates</a></li>
<li class="toctree-l1"><a class="reference internal" href="analyze_variant_counts.html">Counts of variants</a></li>
<li class="toctree-l1"><a class="reference internal" href="analyze_prob_escape.html">Probabilities of escape and neutralization in antibody selections</a></li>
<li class="toctree-l1"><a class="reference internal" href="fit_polyclonal.html">Fit <code class="docutils literal notranslate"><span class="pre">polyclonal</span></code> models</a></li>
<li class="toctree-l1"><a class="reference internal" href="avg_antibody_escape.html">Antibody-escape averaged across replicates</a></li>
</ul>
</div>
</section>
<section id="data-files">
<h2>Data files<a class="headerlink" href="#data-files" title="Permalink to this heading">¶</a></h2>
<ul class="simple">
<li><p><a class="reference external" href="https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/gene_sequence/codon.fasta">parental gene sequence</a></p></li>
<li><p><a class="reference external" href="https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/gene_sequence/protein.fasta">parental protein sequence</a></p></li>
<li><p><a class="reference external" href="https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/data/site_numbering_map.csv">sequential-to-reference site numbers</a></p></li>
<li><p><a class="reference external" href="https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/variants/codon_variants.csv">codon-variant table</a></p></li>
<li><p><a class="reference external" href="https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/barcode_runs/processed_barcode_runs.csv">processed barcode sequencing runs</a></p></li>
<li><p><a class="reference external" href="https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/variant_counts">variant counts</a></p></li>
<li><p><a class="reference external" href="https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/func_scores/functional_selections.csv">functional selection experiments</a></p></li>
<li><p><a class="reference external" href="https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/globalepistasis_fits">mutation effects for each functional selection</a></p></li>
<li><p><a class="reference external" href="https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/muteffects_functional/muteffects_observed.csv">mutation functional effects replicate average (observed phenotype)</a></p></li>
<li><p><a class="reference external" href="https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/muteffects_functional/muteffects_latent.csv">mutation functional effects replicate average (latent phenotype)</a></p></li>
<li><p><a class="reference external" href="https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/prob_escape/antibody_selections.csv">antibody selection experiments</a></p></li>
<li><p><a class="reference external" href="https://github.com/dms-vep/dms-vep-pipeline/blob/main/test_example/results/antibody_escape">antibody escape values</a></p></li>
</ul>
</section>
<section id="interactive-plots-of-mutation-functional-effects">
<h2>Interactive plots of mutation functional effects<a class="headerlink" href="#interactive-plots-of-mutation-functional-effects" title="Permalink to this heading">¶</a></h2>
<ul class="simple">
<li><p><a class="reference external" href="muteffects_observed_heatmap.html">Observed phenotype effects</a></p></li>
<li><p><a class="reference external" href="muteffects_latent_heatmap.html">Latent phenotype effects</a></p></li>
</ul>
</section>
<section id="interactive-plots-of-mutation-antibody-escape">
<h2>Interactive plots of mutation antibody escape<a class="headerlink" href="#interactive-plots-of-mutation-antibody-escape" title="Permalink to this heading">¶</a></h2>
<ul class="simple">
<li><p><a class="reference external" href="REGN10933_escape_plot.html">REGN10933 escape plot</a></p></li>
<li><p><a class="reference external" href="REGN10933_icXX_plot.html">REGN10933 icXX plot</a></p></li>
<li><p><a class="reference external" href="S2M11_escape_plot.html">S2M11 escape plot</a></p></li>
<li><p><a class="reference external" href="S2M11_icXX_plot.html">S2M11 icXX plot</a></p></li>
</ul>
</section>
</section>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
©Jesse Bloom (2023).
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 6.1.3</a>
& <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
|
<a href="_sources/index.rst.txt"
rel="nofollow">Page source</a>
</div>
</body>
</html>