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ime-tools

Tools needed for our work; Logo derived from https://openclipart.org/detail/19214/tools

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

ime-tools

Tools needed for our work; Logo derived from https://openclipart.org/detail/19214/tools

Popular repositories
Loading
  1. 
trimgalore
trimgalorePublic
    Shell
1

  2. 
omniCLIP_docker
omniCLIP_dockerPublic
    
docker file for creating omniCLIP Docker Container

    Shell
1

1

  3. 
poretools
poretoolsPublic
    
Forked from arq5x/poretools
    
a toolkit for working with Oxford nanopore data

    Jupyter Notebook
  4. 
trimmomatic
trimmomaticPublic
  5. 
HISAT2
HISAT2Public
    
Docker container for HISAT2

  6. 
cufflinks
cufflinksPublic
    
Container for cufflinks


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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;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
ime-tools · GitHub
Skip to content
@ime-tools

ime-tools

Tools needed for our work; Logo derived from https://openclipart.org/detail/19214/tools

Popular repositories
Loading
  1. 
trimgalore
trimgalorePublic
    Shell
1

  2. 
omniCLIP_docker
omniCLIP_dockerPublic
    
docker file for creating omniCLIP Docker Container

    Shell
1

1

  3. 
poretools
poretoolsPublic
    
Forked from arq5x/poretools
    
a toolkit for working with Oxford nanopore data

    Jupyter Notebook
  4. 
trimmomatic
trimmomaticPublic
  5. 
HISAT2
HISAT2Public
    
Docker container for HISAT2

  6. 
cufflinks
cufflinksPublic
    
Container for cufflinks


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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('^' + ".*" + '
ime-tools · GitHub
Skip to content
@ime-tools

ime-tools

Tools needed for our work; Logo derived from https://openclipart.org/detail/19214/tools

Popular repositories
Loading
  1. 
trimgalore
trimgalorePublic
    Shell
1

  2. 
omniCLIP_docker
omniCLIP_dockerPublic
    
docker file for creating omniCLIP Docker Container

    Shell
1

1

  3. 
poretools
poretoolsPublic
    
Forked from arq5x/poretools
    
a toolkit for working with Oxford nanopore data

    Jupyter Notebook
  4. 
trimmomatic
trimmomaticPublic
  5. 
HISAT2
HISAT2Public
    
Docker container for HISAT2

  6. 
cufflinks
cufflinksPublic
    
Container for cufflinks


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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" + '
ime-tools · GitHub
Skip to content
@ime-tools

ime-tools

Tools needed for our work; Logo derived from https://openclipart.org/detail/19214/tools

Popular repositories
Loading
  1. 
trimgalore
trimgalorePublic
    Shell
1

  2. 
omniCLIP_docker
omniCLIP_dockerPublic
    
docker file for creating omniCLIP Docker Container

    Shell
1

1

  3. 
poretools
poretoolsPublic
    
Forked from arq5x/poretools
    
a toolkit for working with Oxford nanopore data

    Jupyter Notebook
  4. 
trimmomatic
trimmomaticPublic
  5. 
HISAT2
HISAT2Public
    
Docker container for HISAT2

  6. 
cufflinks
cufflinksPublic
    
Container for cufflinks


Repositories

Showing 10 of 15 repositories
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Top languages
Loading…
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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('^' + ".*" + '
ime-tools · GitHub
Skip to content
@ime-tools

ime-tools

Tools needed for our work; Logo derived from https://openclipart.org/detail/19214/tools

Popular repositories
Loading
  1. 
trimgalore
trimgalorePublic
    Shell
1

  2. 
omniCLIP_docker
omniCLIP_dockerPublic
    
docker file for creating omniCLIP Docker Container

    Shell
1

1

  3. 
poretools
poretoolsPublic
    
Forked from arq5x/poretools
    
a toolkit for working with Oxford nanopore data

    Jupyter Notebook
  4. 
trimmomatic
trimmomaticPublic
  5. 
HISAT2
HISAT2Public
    
Docker container for HISAT2

  6. 
cufflinks
cufflinksPublic
    
Container for cufflinks


Repositories

Showing 10 of 15 repositories
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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('^' + ".*" + '
ime-tools · GitHub
Skip to content
@ime-tools

ime-tools

Tools needed for our work; Logo derived from https://openclipart.org/detail/19214/tools

Popular repositories
Loading
  1. 
trimgalore
trimgalorePublic
    Shell
1

  2. 
omniCLIP_docker
omniCLIP_dockerPublic
    
docker file for creating omniCLIP Docker Container

    Shell
1

1

  3. 
poretools
poretoolsPublic
    
Forked from arq5x/poretools
    
a toolkit for working with Oxford nanopore data

    Jupyter Notebook
  4. 
trimmomatic
trimmomaticPublic
  5. 
HISAT2
HISAT2Public
    
Docker container for HISAT2

  6. 
cufflinks
cufflinksPublic
    
Container for cufflinks


Repositories

Showing 10 of 15 repositories
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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); }
})();
})();
ime-tools · GitHub
Skip to content
@ime-tools

ime-tools

Tools needed for our work; Logo derived from https://openclipart.org/detail/19214/tools

Popular repositories
Loading
  1. 
trimgalore
trimgalorePublic
    Shell
1

  2. 
omniCLIP_docker
omniCLIP_dockerPublic
    
docker file for creating omniCLIP Docker Container

    Shell
1

1

  3. 
poretools
poretoolsPublic
    
Forked from arq5x/poretools
    
a toolkit for working with Oxford nanopore data

    Jupyter Notebook
  4. 
trimmomatic
trimmomaticPublic
  5. 
HISAT2
HISAT2Public
    
Docker container for HISAT2

  6. 
cufflinks
cufflinksPublic
    
Container for cufflinks


Repositories

Showing 10 of 15 repositories
View all repositories
Top languages
Loading…
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Loading…