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bioFAM

Our groups develop and apply computational approaches to study molecular variations and their phenotypic consequence.

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  1. MOFA2 MOFA2Public

    Multi-Omics Factor Analysis

    R 420 63

  2. MOFA MOFAPublic

    Multi-Omics Factor Analysis

    R 268 68

  3. mofapy2 mofapy2Public

    Multi-omics factor analysis v2

    Python 68 31

  4. mofaflex mofaflexPublic

    factor models for omics data

    Python 47 3

  5. mofax mofaxPublic

    Work with trained factor models in Python

    Jupyter Notebook 41 17

  6. scDORI scDORIPublic

    scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (eGRNs) from single-cell multiome data (RNA + ATAC).

    Python 35 7

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, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
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(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
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})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
bioFAM · GitHub
Skip to content
@bioFAM

bioFAM

Our groups develop and apply computational approaches to study molecular variations and their phenotypic consequence.

Popular repositories
Loading
  1. 
MOFA2
MOFA2Public
    
Multi-Omics Factor Analysis

    R
420

63

  2. 
MOFA
MOFAPublic
    
Multi-Omics Factor Analysis

    R
268

68

  3. 
mofapy2
mofapy2Public
    
Multi-omics factor analysis v2

    Python
68

31

  4. 
mofaflex
mofaflexPublic
    
factor models for omics data

    Python
47

3

  5. 
mofax
mofaxPublic
    
Work with trained factor models in Python

    Jupyter Notebook
41

17

  6. 
scDORI
scDORIPublic
    
scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (eGRNs) from single-cell multiome data (RNA + ATAC).

    Python
35

7


Repositories

Showing 10 of 17 repositories
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, '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;
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.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
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document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
bioFAM · GitHub
Skip to content
@bioFAM

bioFAM

Our groups develop and apply computational approaches to study molecular variations and their phenotypic consequence.

Popular repositories
Loading
  1. 
MOFA2
MOFA2Public
    
Multi-Omics Factor Analysis

    R
420

63

  2. 
MOFA
MOFAPublic
    
Multi-Omics Factor Analysis

    R
268

68

  3. 
mofapy2
mofapy2Public
    
Multi-omics factor analysis v2

    Python
68

31

  4. 
mofaflex
mofaflexPublic
    
factor models for omics data

    Python
47

3

  5. 
mofax
mofaxPublic
    
Work with trained factor models in Python

    Jupyter Notebook
41

17

  6. 
scDORI
scDORIPublic
    
scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (eGRNs) from single-cell multiome data (RNA + ATAC).

    Python
35

7


Repositories

Showing 10 of 17 repositories
View all repositories
People

This organization has no public members. You must be a member to see who’s a part of this organization.

Top languages
Loading…
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Loading…

, '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')) {
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if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
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style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
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observer.observe(document.body, { childList: true, subtree: true });
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}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
bioFAM · GitHub
Skip to content
@bioFAM

bioFAM

Our groups develop and apply computational approaches to study molecular variations and their phenotypic consequence.

Popular repositories
Loading
  1. 
MOFA2
MOFA2Public
    
Multi-Omics Factor Analysis

    R
420

63

  2. 
MOFA
MOFAPublic
    
Multi-Omics Factor Analysis

    R
268

68

  3. 
mofapy2
mofapy2Public
    
Multi-omics factor analysis v2

    Python
68

31

  4. 
mofaflex
mofaflexPublic
    
factor models for omics data

    Python
47

3

  5. 
mofax
mofaxPublic
    
Work with trained factor models in Python

    Jupyter Notebook
41

17

  6. 
scDORI
scDORIPublic
    
scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (eGRNs) from single-cell multiome data (RNA + ATAC).

    Python
35

7


Repositories

Showing 10 of 17 repositories
View all repositories
People

This organization has no public members. You must be a member to see who’s a part of this organization.

Top languages
Loading…
Most used topics
Loading…

, '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);
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return url;
}
}
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document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
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cleanLinks();
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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" + '
bioFAM · GitHub
Skip to content
@bioFAM

bioFAM

Our groups develop and apply computational approaches to study molecular variations and their phenotypic consequence.

Popular repositories
Loading
  1. 
MOFA2
MOFA2Public
    
Multi-Omics Factor Analysis

    R
420

63

  2. 
MOFA
MOFAPublic
    
Multi-Omics Factor Analysis

    R
268

68

  3. 
mofapy2
mofapy2Public
    
Multi-omics factor analysis v2

    Python
68

31

  4. 
mofaflex
mofaflexPublic
    
factor models for omics data

    Python
47

3

  5. 
mofax
mofaxPublic
    
Work with trained factor models in Python

    Jupyter Notebook
41

17

  6. 
scDORI
scDORIPublic
    
scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (eGRNs) from single-cell multiome data (RNA + ATAC).

    Python
35

7


Repositories

Showing 10 of 17 repositories
View all repositories
People

This organization has no public members. You must be a member to see who’s a part of this organization.

Top languages
Loading…
Most used topics
Loading…

, '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('^' + ".*" + '
bioFAM · GitHub
Skip to content
@bioFAM

bioFAM

Our groups develop and apply computational approaches to study molecular variations and their phenotypic consequence.

Popular repositories
Loading
  1. 
MOFA2
MOFA2Public
    
Multi-Omics Factor Analysis

    R
420

63

  2. 
MOFA
MOFAPublic
    
Multi-Omics Factor Analysis

    R
268

68

  3. 
mofapy2
mofapy2Public
    
Multi-omics factor analysis v2

    Python
68

31

  4. 
mofaflex
mofaflexPublic
    
factor models for omics data

    Python
47

3

  5. 
mofax
mofaxPublic
    
Work with trained factor models in Python

    Jupyter Notebook
41

17

  6. 
scDORI
scDORIPublic
    
scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (eGRNs) from single-cell multiome data (RNA + ATAC).

    Python
35

7


Repositories

Showing 10 of 17 repositories
View all repositories
People

This organization has no public members. You must be a member to see who’s a part of this organization.

Top languages
Loading…
Most used topics
Loading…

, '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); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
bioFAM · GitHub
Skip to content
@bioFAM

bioFAM

Our groups develop and apply computational approaches to study molecular variations and their phenotypic consequence.

Popular repositories
Loading
  1. 
MOFA2
MOFA2Public
    
Multi-Omics Factor Analysis

    R
420

63

  2. 
MOFA
MOFAPublic
    
Multi-Omics Factor Analysis

    R
268

68

  3. 
mofapy2
mofapy2Public
    
Multi-omics factor analysis v2

    Python
68

31

  4. 
mofaflex
mofaflexPublic
    
factor models for omics data

    Python
47

3

  5. 
mofax
mofaxPublic
    
Work with trained factor models in Python

    Jupyter Notebook
41

17

  6. 
scDORI
scDORIPublic
    
scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (eGRNs) from single-cell multiome data (RNA + ATAC).

    Python
35

7


Repositories

Showing 10 of 17 repositories
View all repositories
People

This organization has no public members. You must be a member to see who’s a part of this organization.

Top languages
Loading…
Most used topics
Loading…

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

bioFAM

Our groups develop and apply computational approaches to study molecular variations and their phenotypic consequence.

Popular repositories
Loading
  1. 
MOFA2
MOFA2Public
    
Multi-Omics Factor Analysis

    R
420

63

  2. 
MOFA
MOFAPublic
    
Multi-Omics Factor Analysis

    R
268

68

  3. 
mofapy2
mofapy2Public
    
Multi-omics factor analysis v2

    Python
68

31

  4. 
mofaflex
mofaflexPublic
    
factor models for omics data

    Python
47

3

  5. 
mofax
mofaxPublic
    
Work with trained factor models in Python

    Jupyter Notebook
41

17

  6. 
scDORI
scDORIPublic
    
scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (eGRNs) from single-cell multiome data (RNA + ATAC).

    Python
35

7


Repositories

Showing 10 of 17 repositories
View all repositories
People

This organization has no public members. You must be a member to see who’s a part of this organization.

Top languages
Loading…
Most used topics
Loading…