-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathindex.html
More file actions
141 lines (116 loc) · 10.7 KB
/
Copy pathindex.html
File metadata and controls
141 lines (116 loc) · 10.7 KB
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
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>Multidimensional Nuclear Magnetic Resonance Peak Fitting and Analysis • fitnmr</title>
<script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
<link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Multidimensional Nuclear Magnetic Resonance Peak Fitting and Analysis">
<meta name="description" content="Tools for fitting and analyzing 1D-4D nuclear magnetic resonance spectra with analytical models of peak shapes and peak groups. The package reads spectra in NMRPipe format, builds constrained parameter structures for chemical shifts, line widths, scalar couplings, volumes, and phases, and performs nonlinear least-squares optimization for iterative peak discovery or simultaneous fits across multiple spectra. It also provides methods for visualization, preprocessing, and kinetic analysis of 1D time-series data, including automated phase optimization, solvent suppression, time-domain correction for frequency shifts and line broadening, modeling spectra as linear combinations of two component spectra, and exponential rate fitting.">
<meta property="og:description" content="Tools for fitting and analyzing 1D-4D nuclear magnetic resonance spectra with analytical models of peak shapes and peak groups. The package reads spectra in NMRPipe format, builds constrained parameter structures for chemical shifts, line widths, scalar couplings, volumes, and phases, and performs nonlinear least-squares optimization for iterative peak discovery or simultaneous fits across multiple spectra. It also provides methods for visualization, preprocessing, and kinetic analysis of 1D time-series data, including automated phase optimization, solvent suppression, time-domain correction for frequency shifts and line broadening, modeling spectra as linear combinations of two component spectra, and exponential rate fitting.">
</head>
<body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
<nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
<a class="navbar-brand me-2" href="index.html">fitnmr</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div id="navbar" class="collapse navbar-collapse ms-3">
<ul class="navbar-nav me-auto">
<li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
<li class="nav-item dropdown">
<button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
<ul class="dropdown-menu" aria-labelledby="dropdown-articles">
<li><a class="dropdown-item" href="articles/peak2d_scripts.html">Automated 2D Peak Fitting Scripts</a></li>
<li><a class="dropdown-item" href="articles/peak2d.html">Automated 2D Peak Fitting Code</a></li>
<li><a class="dropdown-item" href="articles/timeseries1d.html">1D Time Series Preprocessing/Two-State Fitting</a></li>
</ul>
</li>
</ul>
<ul class="navbar-nav">
<li class="nav-item"><form class="form-inline" role="search">
<input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
</form></li>
<li class="nav-item"><a class="external-link nav-link" href="https://github.com/smith-group/fitnmr/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
</ul>
</div>
</div>
</nav><div class="container template-home">
<div class="row">
<main id="main" class="col-md-9"><div class="section level1">
<div class="page-header"><h1 id="fitnmr">FitNMR<a class="anchor" aria-label="anchor" href="#fitnmr"></a>
</h1></div>
<p><a href="https://CRAN.R-project.org/package=fitnmr" class="external-link"><img src="https://www.r-pkg.org/badges/version/fitnmr" alt="CRAN version"></a> <a href="https://smith-group.r-universe.dev/fitnmr" class="external-link"><img src="https://smith-group.r-universe.dev/badges/fitnmr" alt="R-universe version"></a> <a href="https://smith-group.r-universe.dev/fitnmr#checktable" class="external-link"><img src="https://smith-group.r-universe.dev/fitnmr/badges/checks" alt="R-universe checks"></a></p>
<p>FitNMR provides tools for fitting and analyzing 1D-4D nuclear magnetic resonance spectra in R.</p>
<div class="section level2">
<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
</h2>
<p>The most recent release of <code>fitnmr</code> can be installed from <a href="https://cran.r-project.org" class="external-link">CRAN</a> using this R command:</p>
<pre><code><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"fitnmr"</span>, repos <span class="op">=</span> <span class="st">"https://cloud.r-project.org"</span><span class="op">)</span></span></code></pre>
<p>The latest developmental version of <code>fitnmr</code> can be installed from the <a href="https://smith-group.r-universe.dev/" class="external-link">Smith Lab R-universe repository</a> using this R command:</p>
<pre><code><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"fitnmr"</span>, repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"https://smith-group.r-universe.dev"</span>, <span class="st">"https://cloud.r-project.org"</span><span class="op">)</span><span class="op">)</span></span></code></pre>
<p>Please look at the <a href="https://smith-group.r-universe.dev/fitnmr#checktable" class="external-link">R-universe check status</a> before using the developmental version.</p>
</div>
<div class="section level2">
<h2 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a>
</h2>
<p>An example of how to use FitNMR for 2D peak fitting of 15N HSQC spectra can be found in the <a href="https://smith-group.github.io/fitnmr/articles/peak2d_scripts.html">Automated 2D Peak Fitting Scripts</a> vignette. This explains how to use FitNMR in a scripted workflow without writing any R code.</p>
<p>For more background on the 2D HSQC fitting algorithms, or if you are comfortable with R code, see the <a href="https://smith-group.github.io/fitnmr/articles/peak2d.html">Automated 2D Peak Fitting Code</a> vignette.</p>
<p>FitNMR has an interface for fitting spectra using tables of nuclei, couplings, and resonances visible in the spectra. An application of this to fitting 1D spectra of free amino acids was described in <a href="https://doi.org/10.5194/mr-5-103-2024" class="external-link">Syed et al. 2024</a>.</p>
<p>Code to entirely reproduce the manuscript is <a href="https://github.com/smith-group/syed2024" class="external-link">available in a GitHub repository</a>. The text and accompanying figures/tables can be compiled from an R Markdown file run from within the browser using the Binder service. See the repository for more details.</p>
<p>There is also functionality for doing 1D NMR data processing using functions that emulate the behavior of NMRPipe. Those were used in <a href="https://doi.org/10.1002/pro.70508" class="external-link">Blejec et al. 2026</a> to preprocess unlabeled 1D protein NMR spectra for quantitative analysis.</p>
<p>See the <a href="https://smith-group.github.io/fitnmr/articles/timeseries1d.html">1D Time Series Preprocessing/Two-State Fitting</a> vignette for more information.</p>
<p>For a roadmap describing the different categories of functions available, see the <a href="https://smith-group.github.io/fitnmr/reference/fitnmr.html">FitNMR Package Overview</a>.</p>
<p>If you are new to R, chapters 1, 2, 5, and 6 of <a href="https://cran.r-project.org/doc/manuals/r-release/R-intro.html" class="external-link">An Introduction to R</a> are highly recommended.</p>
</div>
<div class="section level2">
<h2 id="license">License<a class="anchor" aria-label="anchor" href="#license"></a>
</h2>
<p>FitNMR is released under the GNU Public License version 3.0.</p>
</div>
</div>
</main><aside class="col-md-3"><div class="links">
<h2 data-toc-skip>Links</h2>
<ul class="list-unstyled">
<li><a href="https://cloud.r-project.org/package=fitnmr" class="external-link">View on CRAN</a></li>
<li><a href="https://github.com/smith-group/fitnmr/" class="external-link">Browse source code</a></li>
</ul>
</div>
<div class="license">
<h2 data-toc-skip>License</h2>
<ul class="list-unstyled">
<li><a href="https://www.r-project.org/Licenses/GPL-3" class="external-link">GPL-3</a></li>
</ul>
</div>
<div class="citation">
<h2 data-toc-skip>Citation</h2>
<ul class="list-unstyled">
<li><a href="authors.html#citation">Citing fitnmr</a></li>
</ul>
</div>
<div class="developers">
<h2 data-toc-skip>Developers</h2>
<ul class="list-unstyled">
<li>
<a href="http://smithlab.wesleyan.edu" class="external-link">Colin Smith</a> <br><small class="roles"> Author, maintainer </small> </li>
</ul>
</div>
</aside>
</div>
<footer><div class="pkgdown-footer-left">
<p>Developed by <a href="http://smithlab.wesleyan.edu" class="external-link">Colin Smith</a>.</p>
</div>
<div class="pkgdown-footer-right">
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p>
</div>
</footer>
</div>
</body>
</html>