@smithlabcode

Smith Lab

A computational biology research group at USC
README.md

smithlabcode

This organization is for code produced as a byproduct of our research in computational biology. All our repos can be found here. Our reseaerch covers diverse topics in computational genomics. So our code covers diverse topics. If you have any questions, here are several options:

  • Post your question as an issue in the corresponding repo.
  • Email the author of the code (which in most cases includes myself, Andrew).
  • Email me. My address is in my profile.

We release our code so it might help you. If it's not working properly or optimally, please ask us and we'll do our best to make it work for you.

Pinned Loading

  1. methbasemethbasePublic

    Thousands of high-quality analyzed methylomes.

    1

  2. preseqpreseqPublic

    Software for predicting library complexity and genome coverage in high-throughput sequencing.

    C++ 97 17

  3. falcofalcoPublic

    A tool to assess the quality of sequence read data

    C++ 137 13

  4. ribotricerribotricerPublic

    A tool for accurately detecting actively translating ORFs from Ribo-seq data

    Python 43 10

  5. abismalabismalPublic

    Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

    C++ 20 6

  6. dnmtoolsdnmtoolsPublic

    Tools for analyzing DNA methylation data

    C++ 47 11

Repositories

Showing 10 of 30 repositories
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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" + '

Skip to content
@smithlabcode

Smith Lab

A computational biology research group at USC
README.md
smithlabcode
This organization is for code produced as a byproduct of our research in computational biology.
All our repos can be found here. Our reseaerch covers diverse topics in computational genomics.
So our code covers diverse topics.
If you have any questions, here are several options:
  • Post your question as an issue in the corresponding repo.
  • Email the author of the code (which in most cases includes myself, Andrew).
  • Email me. My address is in my profile.
We release our code so it might help you. If it's not working properly or optimally,
please ask us and we'll do our best to make it work for you.

Pinned
Loading
  1. methbasemethbasePublic
    
Thousands of high-quality analyzed methylomes.

    
1

  2. preseqpreseqPublic
    
Software for predicting library complexity and genome coverage in high-throughput sequencing.

    C++
97

17

  3. falcofalcoPublic
    
A tool to assess the quality of sequence read data

    C++
137

13

  4. ribotricerribotricerPublic
    
A tool for accurately detecting actively translating ORFs from Ribo-seq data

    Python
43

10

  5. abismalabismalPublic
    
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

    C++
20

6

  6. dnmtoolsdnmtoolsPublic
    
Tools for analyzing DNA methylation data

    C++
47

11


Repositories

Showing 10 of 30 repositories
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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('^' + ".*" + '

Skip to content
@smithlabcode

Smith Lab

A computational biology research group at USC
README.md
smithlabcode
This organization is for code produced as a byproduct of our research in computational biology.
All our repos can be found here. Our reseaerch covers diverse topics in computational genomics.
So our code covers diverse topics.
If you have any questions, here are several options:
  • Post your question as an issue in the corresponding repo.
  • Email the author of the code (which in most cases includes myself, Andrew).
  • Email me. My address is in my profile.
We release our code so it might help you. If it's not working properly or optimally,
please ask us and we'll do our best to make it work for you.

Pinned
Loading
  1. methbasemethbasePublic
    
Thousands of high-quality analyzed methylomes.

    
1

  2. preseqpreseqPublic
    
Software for predicting library complexity and genome coverage in high-throughput sequencing.

    C++
97

17

  3. falcofalcoPublic
    
A tool to assess the quality of sequence read data

    C++
137

13

  4. ribotricerribotricerPublic
    
A tool for accurately detecting actively translating ORFs from Ribo-seq data

    Python
43

10

  5. abismalabismalPublic
    
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

    C++
20

6

  6. dnmtoolsdnmtoolsPublic
    
Tools for analyzing DNA methylation data

    C++
47

11


Repositories

Showing 10 of 30 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…

, '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
@smithlabcode

Smith Lab

A computational biology research group at USC
README.md
smithlabcode
This organization is for code produced as a byproduct of our research in computational biology.
All our repos can be found here. Our reseaerch covers diverse topics in computational genomics.
So our code covers diverse topics.
If you have any questions, here are several options:
  • Post your question as an issue in the corresponding repo.
  • Email the author of the code (which in most cases includes myself, Andrew).
  • Email me. My address is in my profile.
We release our code so it might help you. If it's not working properly or optimally,
please ask us and we'll do our best to make it work for you.

Pinned
Loading
  1. methbasemethbasePublic
    
Thousands of high-quality analyzed methylomes.

    
1

  2. preseqpreseqPublic
    
Software for predicting library complexity and genome coverage in high-throughput sequencing.

    C++
97

17

  3. falcofalcoPublic
    
A tool to assess the quality of sequence read data

    C++
137

13

  4. ribotricerribotricerPublic
    
A tool for accurately detecting actively translating ORFs from Ribo-seq data

    Python
43

10

  5. abismalabismalPublic
    
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

    C++
20

6

  6. dnmtoolsdnmtoolsPublic
    
Tools for analyzing DNA methylation data

    C++
47

11


Repositories

Showing 10 of 30 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…

, '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
@smithlabcode

Smith Lab

A computational biology research group at USC
README.md
smithlabcode
This organization is for code produced as a byproduct of our research in computational biology.
All our repos can be found here. Our reseaerch covers diverse topics in computational genomics.
So our code covers diverse topics.
If you have any questions, here are several options:
  • Post your question as an issue in the corresponding repo.
  • Email the author of the code (which in most cases includes myself, Andrew).
  • Email me. My address is in my profile.
We release our code so it might help you. If it's not working properly or optimally,
please ask us and we'll do our best to make it work for you.

Pinned
Loading
  1. methbasemethbasePublic
    
Thousands of high-quality analyzed methylomes.

    
1

  2. preseqpreseqPublic
    
Software for predicting library complexity and genome coverage in high-throughput sequencing.

    C++
97

17

  3. falcofalcoPublic
    
A tool to assess the quality of sequence read data

    C++
137

13

  4. ribotricerribotricerPublic
    
A tool for accurately detecting actively translating ORFs from Ribo-seq data

    Python
43

10

  5. abismalabismalPublic
    
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

    C++
20

6

  6. dnmtoolsdnmtoolsPublic
    
Tools for analyzing DNA methylation data

    C++
47

11


Repositories

Showing 10 of 30 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…

, '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
@smithlabcode

Smith Lab

A computational biology research group at USC
README.md
smithlabcode
This organization is for code produced as a byproduct of our research in computational biology.
All our repos can be found here. Our reseaerch covers diverse topics in computational genomics.
So our code covers diverse topics.
If you have any questions, here are several options:
  • Post your question as an issue in the corresponding repo.
  • Email the author of the code (which in most cases includes myself, Andrew).
  • Email me. My address is in my profile.
We release our code so it might help you. If it's not working properly or optimally,
please ask us and we'll do our best to make it work for you.

Pinned
Loading
  1. methbasemethbasePublic
    
Thousands of high-quality analyzed methylomes.

    
1

  2. preseqpreseqPublic
    
Software for predicting library complexity and genome coverage in high-throughput sequencing.

    C++
97

17

  3. falcofalcoPublic
    
A tool to assess the quality of sequence read data

    C++
137

13

  4. ribotricerribotricerPublic
    
A tool for accurately detecting actively translating ORFs from Ribo-seq data

    Python
43

10

  5. abismalabismalPublic
    
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

    C++
20

6

  6. dnmtoolsdnmtoolsPublic
    
Tools for analyzing DNA methylation data

    C++
47

11


Repositories

Showing 10 of 30 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…

, '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
@smithlabcode

Smith Lab

A computational biology research group at USC
README.md
smithlabcode
This organization is for code produced as a byproduct of our research in computational biology.
All our repos can be found here. Our reseaerch covers diverse topics in computational genomics.
So our code covers diverse topics.
If you have any questions, here are several options:
  • Post your question as an issue in the corresponding repo.
  • Email the author of the code (which in most cases includes myself, Andrew).
  • Email me. My address is in my profile.
We release our code so it might help you. If it's not working properly or optimally,
please ask us and we'll do our best to make it work for you.

Pinned
Loading
  1. methbasemethbasePublic
    
Thousands of high-quality analyzed methylomes.

    
1

  2. preseqpreseqPublic
    
Software for predicting library complexity and genome coverage in high-throughput sequencing.

    C++
97

17

  3. falcofalcoPublic
    
A tool to assess the quality of sequence read data

    C++
137

13

  4. ribotricerribotricerPublic
    
A tool for accurately detecting actively translating ORFs from Ribo-seq data

    Python
43

10

  5. abismalabismalPublic
    
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

    C++
20

6

  6. dnmtoolsdnmtoolsPublic
    
Tools for analyzing DNA methylation data

    C++
47

11


Repositories

Showing 10 of 30 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…

, '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
@smithlabcode

Smith Lab

A computational biology research group at USC
README.md
smithlabcode
This organization is for code produced as a byproduct of our research in computational biology.
All our repos can be found here. Our reseaerch covers diverse topics in computational genomics.
So our code covers diverse topics.
If you have any questions, here are several options:
  • Post your question as an issue in the corresponding repo.
  • Email the author of the code (which in most cases includes myself, Andrew).
  • Email me. My address is in my profile.
We release our code so it might help you. If it's not working properly or optimally,
please ask us and we'll do our best to make it work for you.

Pinned
Loading
  1. methbasemethbasePublic
    
Thousands of high-quality analyzed methylomes.

    
1

  2. preseqpreseqPublic
    
Software for predicting library complexity and genome coverage in high-throughput sequencing.

    C++
97

17

  3. falcofalcoPublic
    
A tool to assess the quality of sequence read data

    C++
137

13

  4. ribotricerribotricerPublic
    
A tool for accurately detecting actively translating ORFs from Ribo-seq data

    Python
43

10

  5. abismalabismalPublic
    
Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.

    C++
20

6

  6. dnmtoolsdnmtoolsPublic
    
Tools for analyzing DNA methylation data

    C++
47

11


Repositories

Showing 10 of 30 repositories
View all repositories
Top languages
Loading…
Most used topics
Loading…