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Commit 83ec752d authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Merge updates into biorepo branch

parents c747da6b 2d60ed65
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3 merge requests!9Develop,!8Repository,!7Develop
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archetypes/sc_data.md 0 → 100644
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---
title: "{{ replace .Name "-" " " | title }}"
description: "Single-Cell RNA-sequencing Data"
name: "(PENDING)"
date: {{ .Date }}
draft: true
weight: ""
type: "custom"
layout: ""
---
**PENDING**
\ No newline at end of file
config.toml
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...@@ -49,18 +49,18 @@ paginate = 10 ...@@ -49,18 +49,18 @@ paginate = 10
weight = 3 weight = 3
identifier = "publications" identifier = "publications"
url = "/publications/" url = "/publications/"
[[menu.main]] # [[menu.main]]
name = "Biorepository" # name = "Biorepository"
pre = "<i class='fas fa-stethoscope fa-fw'></i>" # pre = "<i class='fas fa-stethoscope fa-fw'></i>"
weight = 4 # weight = 4
identifier = "repository" # identifier = "repository"
url = "/repository/" # url = "/repository/"
[[menu.main]] [[menu.main]]
name = "Single-Cell Data" name = "Single-Cell Data"
pre = "<i class='fas fa-chart-bar fa-fw'></i>" pre = "<i class='fas fa-chart-bar fa-fw'></i>"
weight = 5 weight = 5
identifier = "data" identifier = "sc.data"
url = "/data" url = "/sc.data/"
[[menu.main]] [[menu.main]]
name = "Contact" name = "Contact"
pre = "<i class='fas fa-phone fa-fw'></i>" pre = "<i class='fas fa-phone fa-fw'></i>"
......
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---
title: "Single-Cell RNA-seq Data"
date: 2019-06-10T21:49:01-05:00
draft: false
type: "custom"
layout: "data"
---
content/sc.data/_index.md 0 → 100644
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---
title: "Single-Cell RNA-sequencing Data"
date: 2019-05-19T12:09:34-05:00
draft: false
type: "custom"
layout: "sc.data"
---
content/sc.data/hu.bph.pr.md 0 → 100644
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---
title: "Human BPH"
description: "Single-Cell RNA-sequencing Data"
name: "Human BPH (PENDING)"
date: 2019-12-24T22:35:01-06:00
draft: false
weight: "4"
type: "custom"
layout: ""
---
**PENDING**
\ No newline at end of file
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---
title: "Human Prostate Cancer"
description: "Single-Cell RNA-sequencing Data"
name: "Human Prostate Cancer (PENDING)"
date: 2019-12-24T22:35:22-06:00
draft: false
weight: "5"
type: "custom"
layout: ""
---
**PENDING**
\ No newline at end of file
content/sc.data/hu.donor.bl.md 0 → 100644
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---
title: "Human Donor Bladder"
description: "Single-Cell RNA-sequencing Data"
name: "Human Donor Bladder (PENDING)"
date: 2019-12-24T22:35:48-06:00
draft: false
weight: "3"
type: "custom"
layout: ""
---
**PENDING**
\ No newline at end of file
content/sc.data/hu.donor.pr.deep.md 0 → 100644
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---
title: "Human Donor Prostate"
description: "Single-Cell RNA-sequencing Data"
name: "Human Donor (additional sequencing depth of data published in Henry GH. et al, Cell Reports,2018 and projected in UMAP space)"
date: 2019-12-24T21:46:39-06:00
draft: false
weight: "1"
type: "custom"
layout: "hu.donor.deep"
---
content/sc.data/hu.donor.pr.shallow.md 0 → 100644
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---
title: "Human Donor Prostate (shallow)"
description: "Single-Cell RNA-sequencing Data"
name: "Human Donor (original sequencing depth published in Henry GH. et al, Cell Reports,2018)"
date: 2019-12-24T21:46:39-06:00
draft: true
weight: "2"
type: "custom"
layout: "hu.donor.shallow"
---
content/sc.data/mu.bl.md 0 → 100644
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---
title: "Mouse Bladder"
description: "Single-Cell RNA-sequencing Data"
name: "Mouse Bladder (PENDING)"
date: 2019-12-24T22:36:05-06:00
draft: false
weight: "7"
type: "custom"
layout: ""
---
**PENDING**
\ No newline at end of file
content/sc.data/mu.pr.md 0 → 100644
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---
title: "Mouse Prostate"
description: "Single-Cell RNA-sequencing Data"
name: "Mouse Prostate (PENDING)"
date: 2019-12-24T22:36:01-06:00
draft: false
weight: "6"
type: "custom"
layout: ""
---
**PENDING**
\ No newline at end of file
data/scRNAseq_huPr_D/genes.json deleted 100644 → 0
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data/sc_data/hu_donor_pr_deep/genes.json 0 → 100644
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data/sc_data/hu_donor_pr_shallow/genes.json 0 → 100644
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layouts/custom/hu.donor.deep.html 0 → 100644
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{{ partial "header.html" . }}
<div class="header">
<h1>{{ .Title }}</h1>
<h2>{{ .Description }}</h2>
</div>
<div class="content">
{{ .Content }}
</div>
<style>
.content {
margin: 0;
max-width: none;
}
.select {
float: top;
z-index: 1;
top: 0px;
background: #191818;
overflow-x: hidden;
padding: 8px 10px;
}
.columnS {
float: left;
text-align: center;
width: 50%;
}
.columnF {
float: left;
text-align: center;
width: 33.33%;
}
.row:after {
content: "";
display: table;
clear: both;
}
img {
max-width: 100%;
height: auto;
}
@media (max-width: 1000px) {
.columnS {
text-align: right;
width: 100%;
}
.columnF {
width: 100%;
}
br {
display: none;
}
}
</style>
<body>
<div class="select">
<div class="columnS ui-widget">
<label for="gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
<br>
<input id="gene" size="19">
</div>
<div class="columnS">
<label for="populations" style="font-size:18px;">
<b>Select a group of cell populations:</b>
</label>
<br>
<select name="populations" id="populations">
<option selected="selected" value="Population"> Cell Populations</option>
<option>Lineage</option>
<option value="Zone">Prostatic Zone</option>
<option>Patient</option>
</select>
</div>
<br>
<div style="text-align:center">
<button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
</div>
<hr>
<div>
<span style="font-size:16px; font-weight:bold;">Experimental details:</span>
<br>
<span style="font-size:16px;">
Single Cell RNA-Sequencing was conducted on 32,194 cells from peripheral zone and transition zone from
the prostate of three 18-38 year old organ donors using the 10x Genomics platform. The cells were
clustered and identified by correlation of their transcriptomes to known cell types. Gene expression can
be compared by population identity, cell lineage, patient, or dissected prostatic zone. This data is the
result of additional sequencing done on the same samples post publication, and projected in UMAP space.
</span>
</div>
</div>
<div align="center">
<h1 id="label.gene">NO GENE SELECTED</h1>
<h2 id="label.populations"></h2>
<div class="columnF">
<h4 id="label.ClusterVis">
</h3>
<div class="img">
<img id="img.ClusterVis" src="" />
</div>
<br>
</div>
<div class="columnF">
<h4 id="label.Feature">
</h3>
<div class="img">
<img id="img.Feature" src="" />
</div>
<br>
</div>
<div class="columnF">
<h4 id="label.ViolinBox">
</h3>
<div class="img">
<img id="img.ViolinBox" src="" />
</div>
<br>
</div>
</div>
<hr>
<div align="left">
<div><span style="font-size:18px; font-weight:bold;">Publication found at:</span></div>
<div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875"
target="_blank">Cell Reports</a></span></div>
<div><span style="font-size:18px; font-weight:bold;">Raw data found at:</span></div>
<div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403"
target="_blank">GEO:
GSE117403</a></span></div>
<div><span style="font-size:16px;"><a href="https://doi.org/10.25548/W-R8CM" target="_blank">GUDMAP:
W-R8CM</a></span></div>
</div>
</body>
{{ partial "footer.html" . }}
<head>
<link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
<style>
.ui-autocomplete {
max-height: 200px;
overflow-y: auto;
overflow-x: hidden;
}
</style>
<script>
$(function () {
$("#populations").selectmenu({ width: 230 });
});
$(function () {
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_deep.genes }};
var selectedGene = $("#gene").autocomplete({
source: genes.genes,
maxResults: 10,
maxShowItems: 10,
minLength: 1,
});
});
$("#analysis").click(function (event) {
event.preventDefault();
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_deep.genes }};
_gene = $("#gene").val().toUpperCase();
if ($.inArray(_gene, genes.genes) < 0) {
alert("Gene " + _gene + " not exist in the data.")
return
}
document.getElementById("label.gene").innerHTML = _gene
document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization"
var img = document.getElementById("img.ClusterVis");
img.src = "https://s3.us-east-2.amazonaws.com/images.gse117403.deep/images/" + $("#populations").val() + "/umap.png"
document.getElementById("label.Feature").innerHTML = "Feature Plot"
var img = document.getElementById("img.Feature");
img.src = "https://s3.us-east-2.amazonaws.com/images.gse117403.deep/images/umap/" + "genes/" + _gene + "_1.png"
document.getElementById("label.ViolinBox").innerHTML = "Violin Box Plot"
var img = document.getElementById("img.ViolinBox");
img.src = "https://s3.us-east-2.amazonaws.com/images.gse117403.deep/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return (_gene)
});
</script>
</head>
\ No newline at end of file
layouts/custom/data.html → layouts/custom/hu.donor.shallow.html
+ 191
− 0
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{{ partial "header.html" . }} {{ partial "header.html" . }}
<div class="header"> <div class="header">
<h1>{{ .Title }}</h1> <h1>{{ .Title }}</h1>
<h2>{{ .Description }}</h2> <h2>{{ .Description }}</h2>
</div> </div>
<div class="content"> <div class="content">
{{ .Content }} {{ .Content }}
</div> </div>
<style> <style>
.content{ .content {
margin: 0; margin: 0;
max-width: none; max-width: none;
} }
.select {
float: top; .select {
z-index: 1; float: top;
top: 0px; z-index: 1;
background: #191818; top: 0px;
overflow-x: hidden; background: #191818;
padding: 8px 10px; overflow-x: hidden;
} padding: 8px 10px;
.columnS { }
float: left;
text-align: center; .columnS {
width: 33.33%; float: left;
} text-align: center;
.columnF { width: 50%;
float: left; }
text-align: center;
width: 33.33%; .columnF {
} float: left;
.row:after { text-align: center;
content: ""; width: 33.33%;
display: table; }
clear: both;
} .row:after {
img{ content: "";
max-width: 100%; display: table;
height: auto; clear: both;
} }
@media (max-width: 1000px) {
.columnS { img {
text-align: right; max-width: 100%;
width: 100%; height: auto;
} }
.columnF {
width: 100%; @media (max-width: 1000px) {
} .columnS {
br { text-align: right;
display: none; width: 100%;
} }
}
</style> .columnF {
<body> width: 100%;
<div class="select"> }
<div class="columnS ui-widget">
<label for="gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label> br {
<br> display: none;
<input id="gene" size="19"> }
</div> }
<div class="columnS"> </style>
<label for="lineage" style="font-size:18px;"><b>Select a cell lineage to
display:</b></label> <body>
<br> <div class="select">
<select name="lineage" id="lineage"> <div class="columnS ui-widget">
<option selected="selected" value="all">All Cells</option> <label for="gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
<option value="epi">Epithelial Cells Only</option> <br>
<option value="st">Stromal Cells Only</option> <input id="gene" size="19">
</select> </div>
</div> <div class="columnS">
<div class="columnS"> <label for="populations" style="font-size:18px;">
<label for="populations" style="font-size:18px;"><b>Select a group of cell <b>Select a group of cell populations:</b>
populations:</b></label> </label>
<br> <br>
<select name="populations" id="populations"> <select name="populations" id="populations">
<option>Lineage</option> <option selected="selected" value="Population"> Cell Populations</option>
<option>Patient</option> <option>Lineage</option>
<option selected="selected" value="Populations"> Cell Populations</option> <option value="Zone">Prostatic Zone</option>
<option value="Zone">Prostatic Zone</option> <option>Patient</option>
</select> </select>
</div> </div>
<br> <br>
<button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button> <div style="text-align:center">
<hr> <button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
<div> </div>
<span style="font-size:16px; font-weight:bold;">Experimental details:</span> <hr>
<br> <div>
<span style="font-size:16px;">Single Cell RNA-Sequencing was conducted on <span style="font-size:16px; font-weight:bold;">Experimental details:</span>
32,194 cells from peripheral zone and transition zone from the prostate <br>
of three 18-38 year old organ donors using the 10x Genomics platform. <span style="font-size:16px;">
The cells were clustered and identified by correlation of their Single Cell RNA-Sequencing was conducted on 32,194 cells from peripheral zone and transition zone from the
transcriptomes to known cell types. Gene expression can be compared by prostate of three 18-38 year old organ donors using the 10x Genomics platform. The cells were clustered and
population identity, cell lineage, patient, or dissected prostatic zone.</span> identified by correlation of their transcriptomes to known cell types. Gene expression can be compared by
</div> population identity, cell lineage, patient, or dissected prostatic zone. This is the original sequencing depth
</div> published.
<div align="center"> </span>
<h1 id="label.gene">NO GENE SELECTED</h1> </div>
<h2 id="label.lineage"></h2> </div>
<h3 id="label.populations"></h3> <div align="center">
<div class="columnF"> <h1 id="label.gene">NO GENE SELECTED</h1>
<h4 id="label.ClusterVis"></h3> <h2 id="label.populations"></h2>
<div class="img"> <div class="columnF">
<img id="img.ClusterVis" src="" /> <h4 id="label.ClusterVis">
</div> </h3>
<br> <div class="img">
</div> <img id="img.ClusterVis" src="" />
<div class="columnF"> </div>
<h4 id="label.Feature"></h3> <br>
<div class="img"> </div>
<img id="img.Feature" src="" /> <div class="columnF">
</div> <h4 id="label.Feature">
<br> </h3>
</div> <div class="img">
<div class="columnF"> <img id="img.Feature" src="" />
<h4 id="label.ViolinBox"></h3> </div>
<div class="img"> <br>
<img id="img.ViolinBox" src="" /> </div>
</div> <div class="columnF">
<br> <h4 id="label.ViolinBox">
</div> </h3>
</div> <div class="img">
<hr> <img id="img.ViolinBox" src="" />
<div align="left"> </div>
<div><span style="font-size:18px; font-weight:bold;">Publication found at:</span></div> <br>
<div><span style="font-size:16px;"> <a </div>
href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875" </div>
target="_blank">Cell Reports</a></span></div> <hr>
<div><span style="font-size:18px; font-weight:bold;">Raw data found at:</span></div> <div align="left">
<div><span style="font-size:16px;"> <a <div><span style="font-size:18px; font-weight:bold;">Publication found at:</span></div>
href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403" <div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875"
target="_blank">GEO: target="_blank">Cell Reports</a></span></div>
GSE117403</a></span></div> <div><span style="font-size:18px; font-weight:bold;">Raw data found at:</span></div>
<div><span style="font-size:16px;"><a <div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403"
href="https://doi.org/10.25548/W-R8CM" target="_blank">GUDMAP: W-R8CM</a></span></div> target="_blank">GEO:
</div> GSE117403</a></span></div>
</body> <div><span style="font-size:16px;"><a href="https://doi.org/10.25548/W-R8CM" target="_blank">GUDMAP:
W-R8CM</a></span></div>
</div>
<head> </body>
<link rel="stylesheet"
href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css"> {{ partial "footer.html" . }}
<script
src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script> <head>
<script <link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script> <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
<style> <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
.ui-autocomplete { <style>
max-height: 200px; .ui-autocomplete {
overflow-y: auto; max-height: 200px;
overflow-x: hidden; overflow-y: auto;
} overflow-x: hidden;
</style> }
<script> </style>
$(function(){ <script>
$("#lineage" ).selectmenu({width: 230}); $(function () {
}); $("#populations").selectmenu({ width: 230 });
$(function(){ });
$("#populations" ).selectmenu({width: 230}); $(function () {
}); var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
$(function(){ var selectedGene = $("#gene").autocomplete({
var genes = {{ index .Site.Data.scRNAseq_huPr_D.genes }}; source: genes.genes,
var selectedGene = $("#gene").autocomplete({ maxResults: 10,
source: genes.genes, maxShowItems: 10,
maxResults: 10, minLength: 1,
maxShowItems: 10, });
minLength: 1, });
}); $("#analysis").click(function (event) {
}); event.preventDefault();
$("#analysis").click(function (event) { var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
event.preventDefault(); _gene = $("#gene").val().toUpperCase();
var genes = {{ index .Site.Data.scRNAseq_huPr_D.genes }}; if ($.inArray(_gene, genes.genes) < 0) {
_gene = $("#gene").val().toUpperCase(); alert("Gene " + _gene + " not exist in the data.")
if($.inArray(_gene,genes.genes) < 0){ return
alert("Gene "+ _gene +" not exist in the data.") }
return document.getElementById("label.gene").innerHTML = _gene
} document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
<!-- alert(_gene) --> document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization"
document.getElementById("label.gene").innerHTML = _gene var img = document.getElementById("img.ClusterVis");
document.getElementById("label.lineage").innerHTML = $("#lineage").val().toUpperCase() + " Cells" img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/" + $("#populations").val() + "/tsne.png"
document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase() document.getElementById("label.Feature").innerHTML = "Feature Plot"
document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization" var img = document.getElementById("img.Feature");
var img = document.getElementById("img.ClusterVis"); img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/tsne/" + "genes/" + _gene + "_1.png"
img.src="https://s3.us-east-2.amazonaws.com/data-10.1016-j.celrep.2018.11.086/ID/" + $("#lineage").val() + "/" + $("#populations").val() + "/ClusterVis.png" document.getElementById("label.ViolinBox").innerHTML = "Violin Box Plot"
document.getElementById("label.Feature").innerHTML = "Feature Plot" var img = document.getElementById("img.ViolinBox");
var img = document.getElementById("img.Feature"); img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
img.src="https://s3.us-east-2.amazonaws.com/data-10.1016-j.celrep.2018.11.086/Feature/" + $("#lineage").val() + "/genes/" + _gene + ".png" return (_gene)
document.getElementById("label.ViolinBox").innerHTML = "Violin Box Plot" });
var img = document.getElementById("img.ViolinBox"); </script>
img.src="https://s3.us-east-2.amazonaws.com/data-10.1016-j.celrep.2018.11.086/ViolinBox/" + $("#lineage").val() + "/" + $("#populations").val() + "/" + _gene + ".png" </head>
return(_gene) \ No newline at end of file
});
</script>
</head>
{{ partial "footer.html" . }}
layouts/custom/sc.data.html 0 → 100644
+ 14
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{{ partial "header.html" . }}
<div class="header">
<h1>{{ .Title }}</h1>
<h2>{{ .Description }}</h2>
</div>
<div class="content">
{{ range .Pages.ByWeight }}
<li><a href="{{.Permalink}}">{{.Params.name}}</a></li>
{{ end }}
</div>
{{ partial "footer.html" . }}
\ No newline at end of file
layouts/partials/social.html
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<div class="pure-menu social"> <div class="pure-menu social">
<ul class="pure-menu-list"> <ul class="pure-menu-list">
{{ if .OutputFormats.Get "RSS" }}
<li class="pure-menu-item">
<a class="pure-menu-link" href='{{ with .OutputFormats.Get "RSS" }}{{ .RelPermalink }}{{ end }}'><i
class="fas fa-rss"></i>RSS</a>
</li>
{{ end }}
<!-- SNS microblogging --> <!-- SNS microblogging -->
{{ with .Site.Social.twitter }} {{ with .Site.Social.twitter }}
......
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