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EGC Analysis Documentation Website

https://EpigenomicsCode.github.io/egc-analysis-docs (may not be deployed yet)

Dependencies

Docusaurus is powered by NodeJS. You can set it up with the following conda command:

conda create -n docusaurus -c conda-forge nodejs

After creating the environment above (do this once per machine), you can activate the environment anytime using

conda activate docusaurus

Docusaurus Instructions

This website is built using Docusaurus, a modern static website generator. Use the following commands from within the repo directory (cd /your/path/to/egc-analysis-docs).

Installation

yarn

Local Development

yarn start

This command starts a local development server and opens up a browser window. Most changes are reflected live without having to restart the server.

Build

yarn build

This command generates static content into the build directory and can be served using any static contents hosting service.

Deployment

Using SSH:

USE_SSH=true yarn deploy

Not using SSH:

GIT_USER=<Your GitHub username> yarn deploy

If you are using GitHub pages for hosting, this command is a convenient way to build the website and push to the gh-pages branch.

About

tutorials and analysis ideas for epigenomics data

Resources

Readme
MIT license
Activity
Custom properties

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0 stars

Watchers

0 watching

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0 forks
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, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
 blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
GitHub - EpiGenomicsCode/egc-analysis-docs: tutorials and analysis ideas for epigenomics data · GitHub
Skip to content
BranchesTags
Repository files navigation
EGC Analysis Documentation Website
https://EpigenomicsCode.github.io/egc-analysis-docs (may not be deployed yet)
Dependencies
Docusaurus is powered by NodeJS. You can set it up with the following conda command:
conda create -n docusaurus -c conda-forge nodejs

After creating the environment above (do this once per machine), you can activate the environment anytime using
conda activate docusaurus

Docusaurus Instructions
This website is built using Docusaurus, a modern static website generator. Use the following commands from within the repo directory (cd /your/path/to/egc-analysis-docs).
Installation
yarn
Local Development
yarn start
This command starts a local development server and opens up a browser window. Most changes are reflected live without having to restart the server.
Build
yarn build
This command generates static content into the build directory and can be served using any static contents hosting service.
Deployment
Using SSH:
USE_SSH=true yarn deploy
Not using SSH:
GIT_USER=<Your GitHub username> yarn deploy
If you are using GitHub pages for hosting, this command is a convenient way to build the website and push to the gh-pages branch.
About
tutorials and analysis ideas for epigenomics data
Resources
Readme
MIT license
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - EpiGenomicsCode/egc-analysis-docs: tutorials and analysis ideas for epigenomics data · GitHub
Skip to content
BranchesTags
Repository files navigation
EGC Analysis Documentation Website
https://EpigenomicsCode.github.io/egc-analysis-docs (may not be deployed yet)
Dependencies
Docusaurus is powered by NodeJS. You can set it up with the following conda command:
conda create -n docusaurus -c conda-forge nodejs

After creating the environment above (do this once per machine), you can activate the environment anytime using
conda activate docusaurus

Docusaurus Instructions
This website is built using Docusaurus, a modern static website generator. Use the following commands from within the repo directory (cd /your/path/to/egc-analysis-docs).
Installation
yarn
Local Development
yarn start
This command starts a local development server and opens up a browser window. Most changes are reflected live without having to restart the server.
Build
yarn build
This command generates static content into the build directory and can be served using any static contents hosting service.
Deployment
Using SSH:
USE_SSH=true yarn deploy
Not using SSH:
GIT_USER=<Your GitHub username> yarn deploy
If you are using GitHub pages for hosting, this command is a convenient way to build the website and push to the gh-pages branch.
About
tutorials and analysis ideas for epigenomics data
Resources
Readme
MIT license
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - EpiGenomicsCode/egc-analysis-docs: tutorials and analysis ideas for epigenomics data · GitHub
Skip to content
BranchesTags
Repository files navigation
EGC Analysis Documentation Website
https://EpigenomicsCode.github.io/egc-analysis-docs (may not be deployed yet)
Dependencies
Docusaurus is powered by NodeJS. You can set it up with the following conda command:
conda create -n docusaurus -c conda-forge nodejs

After creating the environment above (do this once per machine), you can activate the environment anytime using
conda activate docusaurus

Docusaurus Instructions
This website is built using Docusaurus, a modern static website generator. Use the following commands from within the repo directory (cd /your/path/to/egc-analysis-docs).
Installation
yarn
Local Development
yarn start
This command starts a local development server and opens up a browser window. Most changes are reflected live without having to restart the server.
Build
yarn build
This command generates static content into the build directory and can be served using any static contents hosting service.
Deployment
Using SSH:
USE_SSH=true yarn deploy
Not using SSH:
GIT_USER=<Your GitHub username> yarn deploy
If you are using GitHub pages for hosting, this command is a convenient way to build the website and push to the gh-pages branch.
About
tutorials and analysis ideas for epigenomics data
Resources
Readme
MIT license
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
GitHub - EpiGenomicsCode/egc-analysis-docs: tutorials and analysis ideas for epigenomics data · GitHub
Skip to content
BranchesTags
Repository files navigation
EGC Analysis Documentation Website
https://EpigenomicsCode.github.io/egc-analysis-docs (may not be deployed yet)
Dependencies
Docusaurus is powered by NodeJS. You can set it up with the following conda command:
conda create -n docusaurus -c conda-forge nodejs

After creating the environment above (do this once per machine), you can activate the environment anytime using
conda activate docusaurus

Docusaurus Instructions
This website is built using Docusaurus, a modern static website generator. Use the following commands from within the repo directory (cd /your/path/to/egc-analysis-docs).
Installation
yarn
Local Development
yarn start
This command starts a local development server and opens up a browser window. Most changes are reflected live without having to restart the server.
Build
yarn build
This command generates static content into the build directory and can be served using any static contents hosting service.
Deployment
Using SSH:
USE_SSH=true yarn deploy
Not using SSH:
GIT_USER=<Your GitHub username> yarn deploy
If you are using GitHub pages for hosting, this command is a convenient way to build the website and push to the gh-pages branch.
About
tutorials and analysis ideas for epigenomics data
Resources
Readme
MIT license
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - EpiGenomicsCode/egc-analysis-docs: tutorials and analysis ideas for epigenomics data · GitHub
Skip to content
BranchesTags
Repository files navigation
EGC Analysis Documentation Website
https://EpigenomicsCode.github.io/egc-analysis-docs (may not be deployed yet)
Dependencies
Docusaurus is powered by NodeJS. You can set it up with the following conda command:
conda create -n docusaurus -c conda-forge nodejs

After creating the environment above (do this once per machine), you can activate the environment anytime using
conda activate docusaurus

Docusaurus Instructions
This website is built using Docusaurus, a modern static website generator. Use the following commands from within the repo directory (cd /your/path/to/egc-analysis-docs).
Installation
yarn
Local Development
yarn start
This command starts a local development server and opens up a browser window. Most changes are reflected live without having to restart the server.
Build
yarn build
This command generates static content into the build directory and can be served using any static contents hosting service.
Deployment
Using SSH:
USE_SSH=true yarn deploy
Not using SSH:
GIT_USER=<Your GitHub username> yarn deploy
If you are using GitHub pages for hosting, this command is a convenient way to build the website and push to the gh-pages branch.
About
tutorials and analysis ideas for epigenomics data
Resources
Readme
MIT license
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
})();
GitHub - EpiGenomicsCode/egc-analysis-docs: tutorials and analysis ideas for epigenomics data · GitHub
Skip to content
BranchesTags
Repository files navigation
EGC Analysis Documentation Website
https://EpigenomicsCode.github.io/egc-analysis-docs (may not be deployed yet)
Dependencies
Docusaurus is powered by NodeJS. You can set it up with the following conda command:
conda create -n docusaurus -c conda-forge nodejs

After creating the environment above (do this once per machine), you can activate the environment anytime using
conda activate docusaurus

Docusaurus Instructions
This website is built using Docusaurus, a modern static website generator. Use the following commands from within the repo directory (cd /your/path/to/egc-analysis-docs).
Installation
yarn
Local Development
yarn start
This command starts a local development server and opens up a browser window. Most changes are reflected live without having to restart the server.
Build
yarn build
This command generates static content into the build directory and can be served using any static contents hosting service.
Deployment
Using SSH:
USE_SSH=true yarn deploy
Not using SSH:
GIT_USER=<Your GitHub username> yarn deploy
If you are using GitHub pages for hosting, this command is a convenient way to build the website and push to the gh-pages branch.
About
tutorials and analysis ideas for epigenomics data
Resources
Readme
MIT license
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages