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@iamandreatonina
iamandreatonina committed Oct 16, 2023
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14 changes: 13 additions & 1 deletion css/main.css
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background-color: #192a45;
color: white;
font-size: small;
}
}

.indexes2{
background-color: #192a45;
color: white;
}

.logo{
border-radius: 50%;
width: 170px;
height: 120px;

}
90 changes: 85 additions & 5 deletions index.html
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<link rel="stylesheet" href="css/main.css">
</head>
<body class="body_style">
<h1 align="center" class="header"> BroadBand <section align = 'right'>
<a href="pages_html/overview.html" class="indexes">Overview</a>
<a href="pages_html/SNV.html" class="indexes">SNVs</a>
<a href="pages_html/SCNA.html" class="indexes">SCNAs</a>
</section> </h1>
<section align="left" style="padding: 0%;">
<a href="./index.html"><img src="./brcApp/www/logo_app.jpg" alt="BroadBand logo" class="logo"></a>
</section>
<h1 align="center" class="header" style="padding-top:0;"> BroadBand
<section align = 'center'>
<a href="pages_html/overview.html" class="indexes">Overview</a>
<a href="pages_html/SNV.html" class="indexes">SNVs</a>
<a href="pages_html/SCNA.html" class="indexes">SCNAs</a>
</section> </h1>
<p style="font-size:medium; padding-left:50px; padding-right:50px ; padding-top:auto; padding-bottom: auto;" > BroadBand is a web-based resource developed with the Shiny R framework,
designed for the exploration of genomic data selected among a comprehensive selection of
breast cancer (BRCA) studies with available information on somatic single nucleotide variants (SNVs) and somatic
copy number alterations (SCNAs). BroadBand allows an intuitive and custom navigation of SNVs and SCNAs data which can
be filtered and summarized at different resolution levels, from gene to chromosome, and stratified across the different breast
cancer histotypes and tumor classifications.</p>
<p style="font-size:medium; padding-left:50px; padding-right:50px ; padding-top:auto; padding-bottom: auto;"> The developed resource takes as input selected pre-processed somatic
single nucleotides alterations and copy number aberrations data from publicly available datasets
(Table 1) to assess the most frequently aberrant genomic regions, from gene- to chromosome-level,
across BRCA tumor subtypes.
The web-resource, organized in 3 different sections, allows the user to explore, visualize and
download information of interest. Each section reports results of a specific analysis that can be
customized by tuning multiple settings.
The first section provides a data overview of considered datasets, reporting a) annotations about
genomic data availability and tumor classification, b) overall summary statistics such as the number
of samples stratified by tumor molecular subtypes. The second section focuses on gene aberration
frequencies based on somatic single nucleotide variants while the third section analyses somatic copy
number alterations and compute aberration frequencies at different resolutions: from gene to
chromosome level.</p>
<p style="font-size:medium; padding-left:50px; padding-right:50px ; padding-top:auto; padding-bottom: auto;"> Breast cancers (BRCA) datasets of interest have been selected and inspected through the
<a href="https://www.cbioportal.org" class="indexes2" target="_blank">cBioPortal</a> for Cancer Genomics resource. The selected studies consist of cohorts
where tumor samples from BRCA oncological patients have been molecularly profiled via Whole
Exome Sequencing (WES) approach.</p>
<table border="1px solid white" style="width:90%;" align="center">
<tr>
<th>Names</th>
<th>Number of patients</th>
<th>Paper references</th>
<th>PMID</th>
</tr>
<tr>
<td>brca_metabric</td>
<td>1980</td>
<td>Breast Cancer (METABRIC,
Nature 2012 & Nat Commun
2016)</td>
<td>27161491,
30867590,
22522925</td>
</tr>
<tr>
<td>brca_igr_2015</td>
<td>208</td>
<td>Metastatic breast cancer
(INSERM-PLoS Med 2016)</td>
<td>28027327</td>
</tr>
<tr>
<td>brca_mbcproject_wagle_2
017</td>
<td>106</td>
<td>The Metastatic Breast Cancer
Project (Provisional -
February 2020)</td>
<td><a href="https://mbcproject.org/data-release" class="indexes2" target="_blank">link</a></td>
</tr>
<tr>
<td>breast_msk_2018</td>
<td>1739</td>
<td>MSK-IMPACT Clinical
sequencing Cohort (MSKK,
Nat Med 2017)</td>
<td>28481359</td>
</tr>
<tr>
<td>brca-tcga_pan_can_atlas_2018</td>
<td>945</td>
<td>Breast Invasive Carcinoma
(TCGA, PanCancer Atlas)</td>
<td>29625048,
29596782,
29622463,
29617662,
29625055,
29625050,
29617662,
30643250,
32214244,
29625049,
29850653</td>
</tr>
</table>
<!-- <div align="center">Hello World!</div> -->
</body>
</html>
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9 changes: 6 additions & 3 deletions pages_html/SCNA.html
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<link rel="stylesheet" href="../css/main.css">
</head>
<body class="body_style">
<section align="left" style="padding: 0%;">
<a href="../index.html"><img src="../brcApp/www/logo_app.jpg" alt="BroadBand logo" class="logo"></a>
</section>
<h1 align="center" class="header">Chromosomal aberrations <div></div> based on SCNAs data
<section align = 'right'>
<section align = 'center'>
<a href="../index.html" class="indexes">BroadBand</a>
<a href="overview.html" class="indexes">Overview</a>
<a href="SNV.html" class="indexes">SNVs</a>
</section></h1>
<p>The third panel is focused on somatic copy number aberrations data, this panel provides a full report
<p style="font-size:medium; padding-left:50px; padding-right:50px ; padding-top:auto; padding-bottom: auto;">The third panel is focused on somatic copy number aberrations data, this panel provides a full report
about the frequencies of somatic copy number aberrations occurring in genomic regions of different
ranges. Specifically, aberrations occurring in gene, chromosomal cytobands and chromosomal arms,
are computed based on molecular features, tumor classification of available data included in the
selected cohorts. </p>
<p>The widget panel (Figure 3A) is populated with multiple selection options which will update the BRCA data displayed by default. Specifically, the widget panel allows the user to:
<p style="font-size:medium; padding-left:50px; padding-right:50px ; padding-top:auto; padding-bottom: auto;">The widget panel (Figure 3A) is populated with multiple selection options which will update the BRCA data displayed by default. Specifically, the widget panel allows the user to:
1. Upload a new BRCA dataset to be inspected in addition to those ones available by default.
The cancel button will reverse the operation by removing the uploaded dataset among
available data.
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9 changes: 6 additions & 3 deletions pages_html/SNV.html
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<link rel="stylesheet" href="../css/main.css">
</head>
<body class="body_style">
<section align="left" style="padding: 0%;">
<a href="../index.html"><img src="../brcApp/www/logo_app.jpg" alt="BroadBand logo" class="logo"></a>
</section>
<h1 align="center" class="header">Genes aberrations frequencies <div></div> based on somatic SNVs data
<section align = 'right'>
<section align = 'center'>
<a href="../index.html" class="indexes">BroadBand</a>
<a href="overview.html" class="indexes">Overview</a>
<a href="SCNA.html" class="indexes">SCNAs</a>
</section></h1>
<p>The second panel is focused on somatic single nucleotide variants data and provides a comprehensive
<p style="font-size:medium; padding-left:50px; padding-right:50px ; padding-top:auto; padding-bottom: auto;">The second panel is focused on somatic single nucleotide variants data and provides a comprehensive
report about the frequencies of aberration of genes </p>
<p>The widget panel (Figure 2A) is populated with multiple selection options which will update the
<p style="font-size:medium; padding-left:50px; padding-right:50px ; padding-top:auto; padding-bottom: auto;">The widget panel (Figure 2A) is populated with multiple selection options which will update the
BRCA data displayed by default. Specifically, the widget panel allows the user to:
1. Upload a new BRCA dataset to be inspected in addition to those ones available by default.
The cancel button will reverse the operation by removing the uploaded dataset among
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9 changes: 6 additions & 3 deletions pages_html/overview.html
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<link rel="stylesheet" href="../css/main.css">
</head>
<body class="body_style">
<section align="left" style="padding: 0%;">
<a href="../index.html"><img src="../brcApp/www/logo_app.jpg" alt="BroadBand logo" class="logo"></a>
</section>
<h1 align="center" class="header">Cohort overview and <div></div> samples stratification
<section align = 'right'>
<section align = 'center'>
<a href="../index.html" class="indexes">BroadBand</a>
<a href="SNV.html"class="indexes">SNVs</a>
<a href="SCNA.html"class="indexes">SCNAs</a>
</section></h1>
<p>The “Overview” panel, the home page of the BroadBand resource, provides a detailed report (as bar
<p style="font-size:medium; padding-left:50px; padding-right:50px ; padding-top:auto; padding-bottom: auto;">The “Overview” panel, the home page of the BroadBand resource, provides a detailed report (as bar
chart and table) about the number of samples, carefully stratified by molecular features and data type
availability, included in the selected cohort(s).</p>
<p>The widget panel (Figure 1A) is populated with multiple selection options which will update the
<p style="font-size:medium; padding-left:50px; padding-right:50px ; padding-top:auto; padding-bottom: auto;">The widget panel (Figure 1A) is populated with multiple selection options which will update the
BRCA data displayed by default. Specifically, the widget panel allows the user to:
1. Upload a new BRCA dataset to be inspected in addition to those ones available by default.
The cancel button will reverse the operation by removing the uploaded dataset among
Expand Down

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