-
Notifications
You must be signed in to change notification settings - Fork 0
/
documentation.html
227 lines (203 loc) · 8.95 KB
/
documentation.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
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
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>OmixHub Documentation</title>
<style>
:root {
--primary-color: #3498db;
--secondary-color: #2c3e50;
--background-color: #ecf0f1;
--text-color: #34495e;
--link-color: #2980b9;
--code-background: #f7f9fa;
}
body {
font-family: 'Arial', sans-serif;
line-height: 1.6;
color: var(--text-color);
background-color: var(--background-color);
margin: 0;
padding: 0;
}
header {
background-color: var(--primary-color);
color: white;
text-align: center;
padding: 1rem 0;
}
nav {
background-color: var(--secondary-color);
padding: 1rem;
}
nav ul {
list-style-type: none;
padding: 0;
display: flex;
justify-content: center;
}
nav ul li {
margin: 0 1rem;
}
nav ul li a {
color: white;
text-decoration: none;
font-weight: bold;
}
main {
max-width: 800px;
margin: 2rem auto;
padding: 0 1rem;
}
section {
background-color: white;
border-radius: 8px;
padding: 2rem;
margin-bottom: 2rem;
box-shadow: 0 4px 6px rgba(0, 0, 0, 0.1);
}
h2 {
color: var(--primary-color);
border-bottom: 2px solid var(--primary-color);
padding-bottom: 0.5rem;
}
h3 {
color: var(--secondary-color);
}
a {
color: var(--link-color);
text-decoration: none;
}
a:hover {
text-decoration: underline;
}
pre {
background-color: var(--code-background);
border-radius: 4px;
padding: 1rem;
overflow-x: auto;
}
code {
font-family: 'Courier New', Courier, monospace;
}
footer {
background-color: var(--secondary-color);
color: white;
text-align: center;
padding: 1rem 0;
margin-top: 2rem;
}
.button {
display: inline-block;
background-color: var(--primary-color);
color: white;
padding: 0.5rem 1rem;
border-radius: 4px;
text-decoration: none;
transition: background-color 0.3s ease;
}
.button:hover {
background-color: var(--link-color);
text-decoration: none;
}
</style>
</head>
<body>
<header>
<h1>OmixHub Documentation</h1>
</header>
<nav>
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="#overview">Overview</a></li>
<li><a href="#getting-started">Getting Started</a></li>
<li><a href="#api-reference">API Reference</a></li>
<li><a href="#examples">Examples</a></li>
<li><a href="#applications">Applications</a></li>
<li><a href="#references">References</a></li>
</ul>
</nav>
<main>
<section id="overview">
<h2>Overview</h2>
<p>OmixHub is a platform that interfaces with GDC using Python to help users apply ML-based analysis on different sequencing data. Currently, we support only RNA-Seq based datasets from the genomic data commons (GDC).</p>
<ul>
<li><strong>Cohort Creation</strong> of Bulk RNA Seq Tumor and Normal Samples from GDC.</li>
<li><strong>Bioinformatics analysis:</strong> Application of PyDESeq2 and GSEA in a single pipeline.</li>
<li><strong>Classical ML analysis:</strong> Applying clustering, supervised ML, and outlier sum statistics.</li>
<li><strong>Custom API Connections:</strong>
<ul>
<li>Search and retrieval of Cancer Data cohorts from GDC using complex JSON filters.</li>
<li>Interacting with MongoDB in a Pythonic manner (DOCS coming soon).</li>
<li>Interacting with Google Cloud BigQuery in a Pythonic manner (DOCS coming soon).</li>
</ul>
</li>
</ul>
</section>
<section id="getting-started">
<h2>Getting Started</h2>
<ol>
<li>Clone the repository:
<pre><code>git clone https://github.com/adhal007/OmixHub.git</code></pre>
</li>
<li>Create the correct conda environment for OmixHub:
<pre><code>conda env create -f environment.yaml</code></pre>
</li>
</ol>
</section>
<section id="api-reference">
<h2>API Reference</h2>
<p>For detailed API reference, please visit the full documentation:</p>
<a href="https://omixhub.readthedocs.io/en/latest/modules.html" class="button">View Full API Reference</a>
</section>
<section id="examples">
<h2>Examples</h2>
<h3>Useful query filters for GDC API endpoints</h3>
<p>For examples of using various filters from the GDCQueryFilters class, please refer to the examples section in the full documentation.</p>
<a href="https://omixhub.readthedocs.io/en/latest/examples.html#useful-query-filters-for-gdc-api-endpoints" class="button">View Query Filter Examples</a>
<h3>Data Processing and Analysis Examples</h3>
<ul>
<li><a href="https://omixhub.readthedocs.io/en/latest/examples.html#cohort-creation-of-bulk-rna-seq-experiments-from-genomic-data-commons-gdc">Cohort Creation of Bulk RNA Seq Experiments from GDC</a></li>
<li><a href="https://omixhub.readthedocs.io/en/latest/examples.html#migrating-gdc-rna-seq-expression-data-to-your-bigquery-database">Migrating GDC RNA-Seq Expression Data to BigQuery</a></li>
<li><a href="https://omixhub.readthedocs.io/en/latest/examples.html#run-an-analysis-for-differential-gene-expression-de-and-gene-set-enrichment-analysis-gsea">Differential Gene Expression and GSEA Analysis</a></li>
<li><a href="https://omixhub.readthedocs.io/en/latest/examples.html#supervised-ml-on-a-dataset-from-bigquery">Supervised ML on a dataset from BigQuery</a></li>
</ul>
</section>
<section id="applications">
<h2>Applications</h2>
<h3>Running Gradio App</h3>
<p>Currently restricted to users. To contribute or try it, contact <a href="mailto:[email protected]">[email protected]</a>.</p>
<p>Running the app:</p>
<pre><code>python3 app_gradio.py</code></pre>
<p>For app navigation documentation, refer to: <code>cd ../tutorial_notebooks/docs/UI Prototype/gradio_use.md</code></p>
</section>
<section id="references">
<h2>References</h2>
<ol>
<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10028977/#S5">Characterizing tumor toxicity in Gene therapy targets from Bulk RNA-Sequencing</a></li>
<li><a href="https://ascopubs.org/doi/10.1200/CCI.19.00095">Bayesian Framework for identifying gene expression outliers in individual sample of RNA-Seq data</a></li>
</ol>
</section>
<section id="additional-docs">
<h2>Additional Documentation</h2>
<ul>
<li><strong>Application Examples</strong>
<ul>
<li><a href="../docs/OutlierMethodsApplication/docs/workflow.md">Outlier sum statistics</a></li>
<li><a href="../docs/SuperviseLearningEnsembleApplication/workflow.md">Supervised ML using Ensemble models on kidney cancer data</a></li>
<li><a href="../docs/UmapApplication/docs/workflow.md">Clustering using bayesian optimized parameters of kidney cancer sub-types from TCGA</a></li>
<li><a href="../notebooks/pydeseq_gsea.ipynb">Analysis of differentially expressed genes functionally</a></li>
</ul>
</li>
<li><a href="../docs/UI%20Prototype/roadmap.md">Roadmap for future developments</a></li>
<li><a href="../src/README.md">Methods in src.Connectors for GDC API search and retrieval using custom queries</a></li>
</ul>
</section>
</main>
<footer>
<p>For the most up-to-date and detailed documentation, please visit: <a href="https://omixhub.readthedocs.io/en/latest/index.html" target="_blank">Full OmixHub Documentation</a></p>
<p>© Copyright 2024, Abhilash Dhal.</p>
</footer>
</body>
</html>