BranchesTags

Repository files navigation

=======================
IGV BINARY DISTRIBUTION
=======================
Prerequisites:
Java 6.0 or greater (http://www.java.com). For MACs this generally means Leopard or Snow Leopard is required. If
you have "Tiger" you can try OpenJDK, although we haven't tested it: http://landonf.bikemonkey.org/static/soylatte/.
Alternatively you can still run IGV 1.5.
Instructions:
1. Download and unzip the distribution file to a directory of your choice.
2. To start IGV execute the following from the command line,
java -Xmx750m -jar igv.jar
Alternatively, you can start IGV with one of the following scripts. You might have to make the script executable
(chmod a+x igv.sh).
igv.bat (for Windows)
igv.sh (for LINUX and MAC OsX)
igv.command (for MAC OsX, double-click to start)
The bat and shell scripts are configured to start IGV with 750MB of
memory. This is a reasonable default for most machines. If you are
working with very large datasets you can increase the amount of memory
available to IGV by editing the first line of the startup script.
Specifically change the value of the "-Xmx" parameter. For example,
to start IGV with 1 gigabyte of memory change the value
-Xmx750m
to -Xmx1000m

About

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

www.broadinstitute.org/igv/

Resources

Readme
Activity

Stars

0 stars

Watchers

1 watching

Forks

0 forks
Report repository

Releases

Packages

Contributors

, '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
=======================
IGV BINARY DISTRIBUTION
=======================
Prerequisites:
Java 6.0 or greater (http://www.java.com). For MACs this generally means Leopard or Snow Leopard is required. If
you have "Tiger" you can try OpenJDK, although we haven't tested it: http://landonf.bikemonkey.org/static/soylatte/.
Alternatively you can still run IGV 1.5.
Instructions:
1. Download and unzip the distribution file to a directory of your choice.
2. To start IGV execute the following from the command line,
java -Xmx750m -jar igv.jar
Alternatively, you can start IGV with one of the following scripts. You might have to make the script executable
(chmod a+x igv.sh).
igv.bat (for Windows)
igv.sh (for LINUX and MAC OsX)
igv.command (for MAC OsX, double-click to start)
The bat and shell scripts are configured to start IGV with 750MB of
memory. This is a reasonable default for most machines. If you are
working with very large datasets you can increase the amount of memory
available to IGV by editing the first line of the startup script.
Specifically change the value of the "-Xmx" parameter. For example,
to start IGV with 1 gigabyte of memory change the value
-Xmx750m
to -Xmx1000m

About
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations 
www.broadinstitute.org/igv/
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors

, '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
=======================
IGV BINARY DISTRIBUTION
=======================
Prerequisites:
Java 6.0 or greater (http://www.java.com). For MACs this generally means Leopard or Snow Leopard is required. If
you have "Tiger" you can try OpenJDK, although we haven't tested it: http://landonf.bikemonkey.org/static/soylatte/.
Alternatively you can still run IGV 1.5.
Instructions:
1. Download and unzip the distribution file to a directory of your choice.
2. To start IGV execute the following from the command line,
java -Xmx750m -jar igv.jar
Alternatively, you can start IGV with one of the following scripts. You might have to make the script executable
(chmod a+x igv.sh).
igv.bat (for Windows)
igv.sh (for LINUX and MAC OsX)
igv.command (for MAC OsX, double-click to start)
The bat and shell scripts are configured to start IGV with 750MB of
memory. This is a reasonable default for most machines. If you are
working with very large datasets you can increase the amount of memory
available to IGV by editing the first line of the startup script.
Specifically change the value of the "-Xmx" parameter. For example,
to start IGV with 1 gigabyte of memory change the value
-Xmx750m
to -Xmx1000m

About
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations 
www.broadinstitute.org/igv/
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors

, '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
=======================
IGV BINARY DISTRIBUTION
=======================
Prerequisites:
Java 6.0 or greater (http://www.java.com). For MACs this generally means Leopard or Snow Leopard is required. If
you have "Tiger" you can try OpenJDK, although we haven't tested it: http://landonf.bikemonkey.org/static/soylatte/.
Alternatively you can still run IGV 1.5.
Instructions:
1. Download and unzip the distribution file to a directory of your choice.
2. To start IGV execute the following from the command line,
java -Xmx750m -jar igv.jar
Alternatively, you can start IGV with one of the following scripts. You might have to make the script executable
(chmod a+x igv.sh).
igv.bat (for Windows)
igv.sh (for LINUX and MAC OsX)
igv.command (for MAC OsX, double-click to start)
The bat and shell scripts are configured to start IGV with 750MB of
memory. This is a reasonable default for most machines. If you are
working with very large datasets you can increase the amount of memory
available to IGV by editing the first line of the startup script.
Specifically change the value of the "-Xmx" parameter. For example,
to start IGV with 1 gigabyte of memory change the value
-Xmx750m
to -Xmx1000m

About
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations 
www.broadinstitute.org/igv/
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors

, '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
=======================
IGV BINARY DISTRIBUTION
=======================
Prerequisites:
Java 6.0 or greater (http://www.java.com). For MACs this generally means Leopard or Snow Leopard is required. If
you have "Tiger" you can try OpenJDK, although we haven't tested it: http://landonf.bikemonkey.org/static/soylatte/.
Alternatively you can still run IGV 1.5.
Instructions:
1. Download and unzip the distribution file to a directory of your choice.
2. To start IGV execute the following from the command line,
java -Xmx750m -jar igv.jar
Alternatively, you can start IGV with one of the following scripts. You might have to make the script executable
(chmod a+x igv.sh).
igv.bat (for Windows)
igv.sh (for LINUX and MAC OsX)
igv.command (for MAC OsX, double-click to start)
The bat and shell scripts are configured to start IGV with 750MB of
memory. This is a reasonable default for most machines. If you are
working with very large datasets you can increase the amount of memory
available to IGV by editing the first line of the startup script.
Specifically change the value of the "-Xmx" parameter. For example,
to start IGV with 1 gigabyte of memory change the value
-Xmx750m
to -Xmx1000m

About
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations 
www.broadinstitute.org/igv/
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors

, '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
=======================
IGV BINARY DISTRIBUTION
=======================
Prerequisites:
Java 6.0 or greater (http://www.java.com). For MACs this generally means Leopard or Snow Leopard is required. If
you have "Tiger" you can try OpenJDK, although we haven't tested it: http://landonf.bikemonkey.org/static/soylatte/.
Alternatively you can still run IGV 1.5.
Instructions:
1. Download and unzip the distribution file to a directory of your choice.
2. To start IGV execute the following from the command line,
java -Xmx750m -jar igv.jar
Alternatively, you can start IGV with one of the following scripts. You might have to make the script executable
(chmod a+x igv.sh).
igv.bat (for Windows)
igv.sh (for LINUX and MAC OsX)
igv.command (for MAC OsX, double-click to start)
The bat and shell scripts are configured to start IGV with 750MB of
memory. This is a reasonable default for most machines. If you are
working with very large datasets you can increase the amount of memory
available to IGV by editing the first line of the startup script.
Specifically change the value of the "-Xmx" parameter. For example,
to start IGV with 1 gigabyte of memory change the value
-Xmx750m
to -Xmx1000m

About
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations 
www.broadinstitute.org/igv/
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors

, '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
=======================
IGV BINARY DISTRIBUTION
=======================
Prerequisites:
Java 6.0 or greater (http://www.java.com). For MACs this generally means Leopard or Snow Leopard is required. If
you have "Tiger" you can try OpenJDK, although we haven't tested it: http://landonf.bikemonkey.org/static/soylatte/.
Alternatively you can still run IGV 1.5.
Instructions:
1. Download and unzip the distribution file to a directory of your choice.
2. To start IGV execute the following from the command line,
java -Xmx750m -jar igv.jar
Alternatively, you can start IGV with one of the following scripts. You might have to make the script executable
(chmod a+x igv.sh).
igv.bat (for Windows)
igv.sh (for LINUX and MAC OsX)
igv.command (for MAC OsX, double-click to start)
The bat and shell scripts are configured to start IGV with 750MB of
memory. This is a reasonable default for most machines. If you are
working with very large datasets you can increase the amount of memory
available to IGV by editing the first line of the startup script.
Specifically change the value of the "-Xmx" parameter. For example,
to start IGV with 1 gigabyte of memory change the value
-Xmx750m
to -Xmx1000m

About
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations 
www.broadinstitute.org/igv/
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors

, '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
=======================
IGV BINARY DISTRIBUTION
=======================
Prerequisites:
Java 6.0 or greater (http://www.java.com). For MACs this generally means Leopard or Snow Leopard is required. If
you have "Tiger" you can try OpenJDK, although we haven't tested it: http://landonf.bikemonkey.org/static/soylatte/.
Alternatively you can still run IGV 1.5.
Instructions:
1. Download and unzip the distribution file to a directory of your choice.
2. To start IGV execute the following from the command line,
java -Xmx750m -jar igv.jar
Alternatively, you can start IGV with one of the following scripts. You might have to make the script executable
(chmod a+x igv.sh).
igv.bat (for Windows)
igv.sh (for LINUX and MAC OsX)
igv.command (for MAC OsX, double-click to start)
The bat and shell scripts are configured to start IGV with 750MB of
memory. This is a reasonable default for most machines. If you are
working with very large datasets you can increase the amount of memory
available to IGV by editing the first line of the startup script.
Specifically change the value of the "-Xmx" parameter. For example,
to start IGV with 1 gigabyte of memory change the value
-Xmx750m
to -Xmx1000m

About
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations 
www.broadinstitute.org/igv/
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors