BranchesTags

Repository files navigation

Biolearn

Biolearn enables easy and versatile analyses of biomarkers of aging data. It provides tools to easily load data from publicly available sources like the Gene Expression Omnibus, National Health and Nutrition Examination Survey, and the Framingham Heart Study. Biolearn also contains reference implementations for common aging clock such as the Horvath clock, DunedinPACE and many others that can easily be run in only a few lines of code. You can read more about it in our paper.

Warning

This is a prerelease version of the biolearn library. There may be bugs and interfaces are subject to change.

Important links

Requirements

Python 3.10+

Install

Install biolearn using pip.

pip install biolearn

To verify the library was installed correctly open python or a jupyter notebook and run:

frombiolearn.data_libraryimportDataLibrary

If it executes with no errors then the library is installed. To get started check out some code examples

Discord server

The biolearn team has a discord server to answer questions, discuss feature requests, or have any biolearn related discussions.

Issues

If you find any bugs with biolearn please create a Github issue including how we can replicate the issue and the expected vs actual behavior.

Contributing

Detailed instructions on developer setup and how to contribute are available in the repo

About

Machine learning tools for biomarker analysis

bio-learn.github.io/

Resources

Readme
License
Activity
Custom properties

Stars

91 stars

Watchers

4 watching

Forks

39 forks
Report repository

Releases

Packages

Used by

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n 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;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
BranchesTags
Repository files navigation
Biolearn
Biolearn enables easy and versatile analyses of biomarkers of aging data. It provides tools to easily load data from publicly available sources like the
Gene Expression Omnibus, National Health and Nutrition Examination Survey,
and the Framingham Heart Study. Biolearn also contains reference implementations for common aging clock such as the
Horvath clock, DunedinPACE and many others that can easily be run in only a few lines of code. You can read more about it in our paper.
Warning
This is a prerelease version of the biolearn library. There may be bugs and interfaces are subject to change.
Important links
Requirements
Python 3.10+
Install
Install biolearn using pip.
pip install biolearn
To verify the library was installed correctly open python or a jupyter notebook and run:
frombiolearn.data_libraryimportDataLibrary
If it executes with no errors then the library is installed. To get started check out some code examples
Discord server
The biolearn team has a discord server to answer questions,
discuss feature requests, or have any biolearn related discussions.
Issues
If you find any bugs with biolearn please create a Github issue including how we can replicate the issue and the expected vs actual behavior.
Contributing
Detailed instructions on developer setup and how to contribute are available in the repo
About
Machine learning tools for biomarker analysis
bio-learn.github.io/
Resources
Readme
License
Activity
Custom properties
Stars
91 stars
Watchers
4 watching
Forks
39 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Biolearn
Biolearn enables easy and versatile analyses of biomarkers of aging data. It provides tools to easily load data from publicly available sources like the
Gene Expression Omnibus, National Health and Nutrition Examination Survey,
and the Framingham Heart Study. Biolearn also contains reference implementations for common aging clock such as the
Horvath clock, DunedinPACE and many others that can easily be run in only a few lines of code. You can read more about it in our paper.
Warning
This is a prerelease version of the biolearn library. There may be bugs and interfaces are subject to change.
Important links
Requirements
Python 3.10+
Install
Install biolearn using pip.
pip install biolearn
To verify the library was installed correctly open python or a jupyter notebook and run:
frombiolearn.data_libraryimportDataLibrary
If it executes with no errors then the library is installed. To get started check out some code examples
Discord server
The biolearn team has a discord server to answer questions,
discuss feature requests, or have any biolearn related discussions.
Issues
If you find any bugs with biolearn please create a Github issue including how we can replicate the issue and the expected vs actual behavior.
Contributing
Detailed instructions on developer setup and how to contribute are available in the repo
About
Machine learning tools for biomarker analysis
bio-learn.github.io/
Resources
Readme
License
Activity
Custom properties
Stars
91 stars
Watchers
4 watching
Forks
39 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Biolearn
Biolearn enables easy and versatile analyses of biomarkers of aging data. It provides tools to easily load data from publicly available sources like the
Gene Expression Omnibus, National Health and Nutrition Examination Survey,
and the Framingham Heart Study. Biolearn also contains reference implementations for common aging clock such as the
Horvath clock, DunedinPACE and many others that can easily be run in only a few lines of code. You can read more about it in our paper.
Warning
This is a prerelease version of the biolearn library. There may be bugs and interfaces are subject to change.
Important links
Requirements
Python 3.10+
Install
Install biolearn using pip.
pip install biolearn
To verify the library was installed correctly open python or a jupyter notebook and run:
frombiolearn.data_libraryimportDataLibrary
If it executes with no errors then the library is installed. To get started check out some code examples
Discord server
The biolearn team has a discord server to answer questions,
discuss feature requests, or have any biolearn related discussions.
Issues
If you find any bugs with biolearn please create a Github issue including how we can replicate the issue and the expected vs actual behavior.
Contributing
Detailed instructions on developer setup and how to contribute are available in the repo
About
Machine learning tools for biomarker analysis
bio-learn.github.io/
Resources
Readme
License
Activity
Custom properties
Stars
91 stars
Watchers
4 watching
Forks
39 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BranchesTags
Repository files navigation
Biolearn
Biolearn enables easy and versatile analyses of biomarkers of aging data. It provides tools to easily load data from publicly available sources like the
Gene Expression Omnibus, National Health and Nutrition Examination Survey,
and the Framingham Heart Study. Biolearn also contains reference implementations for common aging clock such as the
Horvath clock, DunedinPACE and many others that can easily be run in only a few lines of code. You can read more about it in our paper.
Warning
This is a prerelease version of the biolearn library. There may be bugs and interfaces are subject to change.
Important links
Requirements
Python 3.10+
Install
Install biolearn using pip.
pip install biolearn
To verify the library was installed correctly open python or a jupyter notebook and run:
frombiolearn.data_libraryimportDataLibrary
If it executes with no errors then the library is installed. To get started check out some code examples
Discord server
The biolearn team has a discord server to answer questions,
discuss feature requests, or have any biolearn related discussions.
Issues
If you find any bugs with biolearn please create a Github issue including how we can replicate the issue and the expected vs actual behavior.
Contributing
Detailed instructions on developer setup and how to contribute are available in the repo
About
Machine learning tools for biomarker analysis
bio-learn.github.io/
Resources
Readme
License
Activity
Custom properties
Stars
91 stars
Watchers
4 watching
Forks
39 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Biolearn
Biolearn enables easy and versatile analyses of biomarkers of aging data. It provides tools to easily load data from publicly available sources like the
Gene Expression Omnibus, National Health and Nutrition Examination Survey,
and the Framingham Heart Study. Biolearn also contains reference implementations for common aging clock such as the
Horvath clock, DunedinPACE and many others that can easily be run in only a few lines of code. You can read more about it in our paper.
Warning
This is a prerelease version of the biolearn library. There may be bugs and interfaces are subject to change.
Important links
Requirements
Python 3.10+
Install
Install biolearn using pip.
pip install biolearn
To verify the library was installed correctly open python or a jupyter notebook and run:
frombiolearn.data_libraryimportDataLibrary
If it executes with no errors then the library is installed. To get started check out some code examples
Discord server
The biolearn team has a discord server to answer questions,
discuss feature requests, or have any biolearn related discussions.
Issues
If you find any bugs with biolearn please create a Github issue including how we can replicate the issue and the expected vs actual behavior.
Contributing
Detailed instructions on developer setup and how to contribute are available in the repo
About
Machine learning tools for biomarker analysis
bio-learn.github.io/
Resources
Readme
License
Activity
Custom properties
Stars
91 stars
Watchers
4 watching
Forks
39 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Biolearn
Biolearn enables easy and versatile analyses of biomarkers of aging data. It provides tools to easily load data from publicly available sources like the
Gene Expression Omnibus, National Health and Nutrition Examination Survey,
and the Framingham Heart Study. Biolearn also contains reference implementations for common aging clock such as the
Horvath clock, DunedinPACE and many others that can easily be run in only a few lines of code. You can read more about it in our paper.
Warning
This is a prerelease version of the biolearn library. There may be bugs and interfaces are subject to change.
Important links
Requirements
Python 3.10+
Install
Install biolearn using pip.
pip install biolearn
To verify the library was installed correctly open python or a jupyter notebook and run:
frombiolearn.data_libraryimportDataLibrary
If it executes with no errors then the library is installed. To get started check out some code examples
Discord server
The biolearn team has a discord server to answer questions,
discuss feature requests, or have any biolearn related discussions.
Issues
If you find any bugs with biolearn please create a Github issue including how we can replicate the issue and the expected vs actual behavior.
Contributing
Detailed instructions on developer setup and how to contribute are available in the repo
About
Machine learning tools for biomarker analysis
bio-learn.github.io/
Resources
Readme
License
Activity
Custom properties
Stars
91 stars
Watchers
4 watching
Forks
39 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
Biolearn
Biolearn enables easy and versatile analyses of biomarkers of aging data. It provides tools to easily load data from publicly available sources like the
Gene Expression Omnibus, National Health and Nutrition Examination Survey,
and the Framingham Heart Study. Biolearn also contains reference implementations for common aging clock such as the
Horvath clock, DunedinPACE and many others that can easily be run in only a few lines of code. You can read more about it in our paper.
Warning
This is a prerelease version of the biolearn library. There may be bugs and interfaces are subject to change.
Important links
Requirements
Python 3.10+
Install
Install biolearn using pip.
pip install biolearn
To verify the library was installed correctly open python or a jupyter notebook and run:
frombiolearn.data_libraryimportDataLibrary
If it executes with no errors then the library is installed. To get started check out some code examples
Discord server
The biolearn team has a discord server to answer questions,
discuss feature requests, or have any biolearn related discussions.
Issues
If you find any bugs with biolearn please create a Github issue including how we can replicate the issue and the expected vs actual behavior.
Contributing
Detailed instructions on developer setup and how to contribute are available in the repo
About
Machine learning tools for biomarker analysis
bio-learn.github.io/
Resources
Readme
License
Activity
Custom properties
Stars
91 stars
Watchers
4 watching
Forks
39 forks
Report repository
Releases
Packages
Used by
Contributors
Languages