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Package: TSimulator
Type: Package
Title: Simulates gene transcription in the gene network/subnetwork provided
Version: 0.83
Date: 2009-09-16
Author: Yeison Rodriguez
Maintainer: Yeison Rodriguez <yeison.rodriguez@nyu.edu>
Description: The simulator takes an interaction network, and outputs a variety of mRNA transcript values for any given period of time. The values are provided by a differential equation solver. This solver evaluates a system of ordinary differential equations. It evaluates the interactions that are occurring at every timestep, in order to approximate transcript values for the next time point. The size of the timestep has a default value, but it may also be provided by the user. The user may also utilize some of the functions to simulate a microarray assay experiment. The goal is to offer a variety of functions, one to model each type of experimental paradigm. The paradigms available will be something along the lines of (a) replication, (b) no replication with closely clustered measurements, (c) no replication with diffuse clustering of measurements.
License: GPLv2
LazyLoad: yes

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, '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" + '

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Package: TSimulator
Type: Package
Title: Simulates gene transcription in the gene network/subnetwork provided
Version: 0.83
Date: 2009-09-16
Author: Yeison Rodriguez
Maintainer: Yeison Rodriguez <yeison.rodriguez@nyu.edu>
Description: The simulator takes an interaction network, and outputs a variety of mRNA transcript values for any given period of time. The values are provided by a differential equation solver. This solver evaluates a system of ordinary differential equations. It evaluates the interactions that are occurring at every timestep, in order to approximate transcript values for the next time point. The size of the timestep has a default value, but it may also be provided by the user. The user may also utilize some of the functions to simulate a microarray assay experiment. The goal is to offer a variety of functions, one to model each type of experimental paradigm. The paradigms available will be something along the lines of (a) replication, (b) no replication with closely clustered measurements, (c) no replication with diffuse clustering of measurements.
License: GPLv2
LazyLoad: yes

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, '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('^' + ".*" + '

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Package: TSimulator
Type: Package
Title: Simulates gene transcription in the gene network/subnetwork provided
Version: 0.83
Date: 2009-09-16
Author: Yeison Rodriguez
Maintainer: Yeison Rodriguez <yeison.rodriguez@nyu.edu>
Description: The simulator takes an interaction network, and outputs a variety of mRNA transcript values for any given period of time. The values are provided by a differential equation solver. This solver evaluates a system of ordinary differential equations. It evaluates the interactions that are occurring at every timestep, in order to approximate transcript values for the next time point. The size of the timestep has a default value, but it may also be provided by the user. The user may also utilize some of the functions to simulate a microarray assay experiment. The goal is to offer a variety of functions, one to model each type of experimental paradigm. The paradigms available will be something along the lines of (a) replication, (b) no replication with closely clustered measurements, (c) no replication with diffuse clustering of measurements.
License: GPLv2
LazyLoad: yes

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, '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('^' + ".*" + '

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Package: TSimulator
Type: Package
Title: Simulates gene transcription in the gene network/subnetwork provided
Version: 0.83
Date: 2009-09-16
Author: Yeison Rodriguez
Maintainer: Yeison Rodriguez <yeison.rodriguez@nyu.edu>
Description: The simulator takes an interaction network, and outputs a variety of mRNA transcript values for any given period of time. The values are provided by a differential equation solver. This solver evaluates a system of ordinary differential equations. It evaluates the interactions that are occurring at every timestep, in order to approximate transcript values for the next time point. The size of the timestep has a default value, but it may also be provided by the user. The user may also utilize some of the functions to simulate a microarray assay experiment. The goal is to offer a variety of functions, one to model each type of experimental paradigm. The paradigms available will be something along the lines of (a) replication, (b) no replication with closely clustered measurements, (c) no replication with diffuse clustering of measurements.
License: GPLv2
LazyLoad: yes

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The evolution of LDE solver to an R package
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, '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" + '

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Package: TSimulator
Type: Package
Title: Simulates gene transcription in the gene network/subnetwork provided
Version: 0.83
Date: 2009-09-16
Author: Yeison Rodriguez
Maintainer: Yeison Rodriguez <yeison.rodriguez@nyu.edu>
Description: The simulator takes an interaction network, and outputs a variety of mRNA transcript values for any given period of time. The values are provided by a differential equation solver. This solver evaluates a system of ordinary differential equations. It evaluates the interactions that are occurring at every timestep, in order to approximate transcript values for the next time point. The size of the timestep has a default value, but it may also be provided by the user. The user may also utilize some of the functions to simulate a microarray assay experiment. The goal is to offer a variety of functions, one to model each type of experimental paradigm. The paradigms available will be something along the lines of (a) replication, (b) no replication with closely clustered measurements, (c) no replication with diffuse clustering of measurements.
License: GPLv2
LazyLoad: yes

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, '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('^' + ".*" + '

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Package: TSimulator
Type: Package
Title: Simulates gene transcription in the gene network/subnetwork provided
Version: 0.83
Date: 2009-09-16
Author: Yeison Rodriguez
Maintainer: Yeison Rodriguez <yeison.rodriguez@nyu.edu>
Description: The simulator takes an interaction network, and outputs a variety of mRNA transcript values for any given period of time. The values are provided by a differential equation solver. This solver evaluates a system of ordinary differential equations. It evaluates the interactions that are occurring at every timestep, in order to approximate transcript values for the next time point. The size of the timestep has a default value, but it may also be provided by the user. The user may also utilize some of the functions to simulate a microarray assay experiment. The goal is to offer a variety of functions, one to model each type of experimental paradigm. The paradigms available will be something along the lines of (a) replication, (b) no replication with closely clustered measurements, (c) no replication with diffuse clustering of measurements.
License: GPLv2
LazyLoad: yes

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The evolution of LDE solver to an R package
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1 watching
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, '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('^' + ".*" + '

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Package: TSimulator
Type: Package
Title: Simulates gene transcription in the gene network/subnetwork provided
Version: 0.83
Date: 2009-09-16
Author: Yeison Rodriguez
Maintainer: Yeison Rodriguez <yeison.rodriguez@nyu.edu>
Description: The simulator takes an interaction network, and outputs a variety of mRNA transcript values for any given period of time. The values are provided by a differential equation solver. This solver evaluates a system of ordinary differential equations. It evaluates the interactions that are occurring at every timestep, in order to approximate transcript values for the next time point. The size of the timestep has a default value, but it may also be provided by the user. The user may also utilize some of the functions to simulate a microarray assay experiment. The goal is to offer a variety of functions, one to model each type of experimental paradigm. The paradigms available will be something along the lines of (a) replication, (b) no replication with closely clustered measurements, (c) no replication with diffuse clustering of measurements.
License: GPLv2
LazyLoad: yes

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The evolution of LDE solver to an R package
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, '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); }
})();
})();

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Package: TSimulator
Type: Package
Title: Simulates gene transcription in the gene network/subnetwork provided
Version: 0.83
Date: 2009-09-16
Author: Yeison Rodriguez
Maintainer: Yeison Rodriguez <yeison.rodriguez@nyu.edu>
Description: The simulator takes an interaction network, and outputs a variety of mRNA transcript values for any given period of time. The values are provided by a differential equation solver. This solver evaluates a system of ordinary differential equations. It evaluates the interactions that are occurring at every timestep, in order to approximate transcript values for the next time point. The size of the timestep has a default value, but it may also be provided by the user. The user may also utilize some of the functions to simulate a microarray assay experiment. The goal is to offer a variety of functions, one to model each type of experimental paradigm. The paradigms available will be something along the lines of (a) replication, (b) no replication with closely clustered measurements, (c) no replication with diffuse clustering of measurements.
License: GPLv2
LazyLoad: yes

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The evolution of LDE solver to an R package
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Stars
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