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For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.

For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.
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Update create_mofa.R by willisbillis · Pull Request #166 · bioFAM/MOFA2 · GitHub
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Update create_mofa.R - #166

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For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.

For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.
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Update create_mofa.R - #166

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For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.

For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.
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, '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('^' + ".*" + ' Update create_mofa.R by willisbillis · Pull Request #166 · bioFAM/MOFA2 · GitHub
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For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.

For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.
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, '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" + ' Update create_mofa.R by willisbillis · Pull Request #166 · bioFAM/MOFA2 · GitHub
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Update create_mofa.R - #166

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For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.

For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.
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, '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('^' + ".*" + ' Update create_mofa.R by willisbillis · Pull Request #166 · bioFAM/MOFA2 · GitHub
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For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.

For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.
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, '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('^' + ".*" + ' Update create_mofa.R by willisbillis · Pull Request #166 · bioFAM/MOFA2 · GitHub
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For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.

For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.
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, '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); } })(); })(); Update create_mofa.R by willisbillis · Pull Request #166 · bioFAM/MOFA2 · GitHub
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Update create_mofa.R - #166

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For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.

For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will result in indexing outside of the range of the smaller modality and throw an error when generating the MOFA object. This ensures that the underrepresented modality is not indexed out of its range.
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