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pyranges

Coverage Statushypothesis testedPyPI versionMITPyPI - Python Versioninstall with bioconda

Introduction

PyRanges is a Python library specifically designed for efficient and intuitive manipulation of genomics data, particularly genomic intervals (like genes, genomic features, or reads). The library is optimized for fast querying and manipulation of genomic annotations.

"Finally ... This was what Python badly needed for years." - Heng Li

Documentation

The pyranges documentation is centralized at https://pyranges.readthedocs.io/ Visit it to find installation instructions, API, tutorial, and how-to-pages.

Features

  • fast
  • memory-efficient
  • featureful
  • pythonic/pandastic
  • supports chaining with a terse syntax
  • uses Pandas DataFrames, so the whole Python data science stack works on PyRanges.

Paper/Cite

Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36(3):918-919http://dx.doi.org/10.1093/bioinformatics/btz615

Supporting pyranges

  • most importantly, cite pyranges if you use it. It is the main metric funding sources care about.
  • use pyranges in Stack Overflow/biostars questions and answers
  • star the repo (possibly important for github visibility and as a proxy for project popularity)
  • if you are a business using pyranges, please give to one of the charities listed at https://www.givewell.org/

About

Performant Pythonic GenomicRanges

pyranges.readthedocs.io

Resources

Readme
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} 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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pyranges
Coverage Statushypothesis testedPyPI versionMITPyPI - Python Versioninstall with bioconda
Introduction
PyRanges is a Python library specifically designed for efficient and intuitive manipulation of genomics data,
particularly genomic intervals (like genes, genomic features, or reads).
The library is optimized for fast querying and manipulation of genomic annotations.
"Finally ... This was what Python badly needed for years." - Heng Li
Documentation
The pyranges documentation is centralized at https://pyranges.readthedocs.io/
Visit it to find installation instructions, API, tutorial, and how-to-pages.
Features
  • fast
  • memory-efficient
  • featureful
  • pythonic/pandastic
  • supports chaining with a terse syntax
  • uses Pandas DataFrames, so the whole Python data science stack works on PyRanges.
Paper/Cite
Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36(3):918-919http://dx.doi.org/10.1093/bioinformatics/btz615
Supporting pyranges
  • most importantly, cite pyranges if you use it. It is the main metric funding sources care about.
  • use pyranges in Stack Overflow/biostars questions and answers
  • star the repo (possibly important for github visibility and as a proxy for project popularity)
  • if you are a business using pyranges, please give to one of the charities listed at https://www.givewell.org/
About
Performant Pythonic GenomicRanges
pyranges.readthedocs.io
Resources
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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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pyranges
Coverage Statushypothesis testedPyPI versionMITPyPI - Python Versioninstall with bioconda
Introduction
PyRanges is a Python library specifically designed for efficient and intuitive manipulation of genomics data,
particularly genomic intervals (like genes, genomic features, or reads).
The library is optimized for fast querying and manipulation of genomic annotations.
"Finally ... This was what Python badly needed for years." - Heng Li
Documentation
The pyranges documentation is centralized at https://pyranges.readthedocs.io/
Visit it to find installation instructions, API, tutorial, and how-to-pages.
Features
  • fast
  • memory-efficient
  • featureful
  • pythonic/pandastic
  • supports chaining with a terse syntax
  • uses Pandas DataFrames, so the whole Python data science stack works on PyRanges.
Paper/Cite
Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36(3):918-919http://dx.doi.org/10.1093/bioinformatics/btz615
Supporting pyranges
  • most importantly, cite pyranges if you use it. It is the main metric funding sources care about.
  • use pyranges in Stack Overflow/biostars questions and answers
  • star the repo (possibly important for github visibility and as a proxy for project popularity)
  • if you are a business using pyranges, please give to one of the charities listed at https://www.givewell.org/
About
Performant Pythonic GenomicRanges
pyranges.readthedocs.io
Resources
Readme
License
Activity
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0 watching
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0 forks
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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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pyranges
Coverage Statushypothesis testedPyPI versionMITPyPI - Python Versioninstall with bioconda
Introduction
PyRanges is a Python library specifically designed for efficient and intuitive manipulation of genomics data,
particularly genomic intervals (like genes, genomic features, or reads).
The library is optimized for fast querying and manipulation of genomic annotations.
"Finally ... This was what Python badly needed for years." - Heng Li
Documentation
The pyranges documentation is centralized at https://pyranges.readthedocs.io/
Visit it to find installation instructions, API, tutorial, and how-to-pages.
Features
  • fast
  • memory-efficient
  • featureful
  • pythonic/pandastic
  • supports chaining with a terse syntax
  • uses Pandas DataFrames, so the whole Python data science stack works on PyRanges.
Paper/Cite
Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36(3):918-919http://dx.doi.org/10.1093/bioinformatics/btz615
Supporting pyranges
  • most importantly, cite pyranges if you use it. It is the main metric funding sources care about.
  • use pyranges in Stack Overflow/biostars questions and answers
  • star the repo (possibly important for github visibility and as a proxy for project popularity)
  • if you are a business using pyranges, please give to one of the charities listed at https://www.givewell.org/
About
Performant Pythonic GenomicRanges
pyranges.readthedocs.io
Resources
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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" + '

Skip to content
BranchesTags
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pyranges
Coverage Statushypothesis testedPyPI versionMITPyPI - Python Versioninstall with bioconda
Introduction
PyRanges is a Python library specifically designed for efficient and intuitive manipulation of genomics data,
particularly genomic intervals (like genes, genomic features, or reads).
The library is optimized for fast querying and manipulation of genomic annotations.
"Finally ... This was what Python badly needed for years." - Heng Li
Documentation
The pyranges documentation is centralized at https://pyranges.readthedocs.io/
Visit it to find installation instructions, API, tutorial, and how-to-pages.
Features
  • fast
  • memory-efficient
  • featureful
  • pythonic/pandastic
  • supports chaining with a terse syntax
  • uses Pandas DataFrames, so the whole Python data science stack works on PyRanges.
Paper/Cite
Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36(3):918-919http://dx.doi.org/10.1093/bioinformatics/btz615
Supporting pyranges
  • most importantly, cite pyranges if you use it. It is the main metric funding sources care about.
  • use pyranges in Stack Overflow/biostars questions and answers
  • star the repo (possibly important for github visibility and as a proxy for project popularity)
  • if you are a business using pyranges, please give to one of the charities listed at https://www.givewell.org/
About
Performant Pythonic GenomicRanges
pyranges.readthedocs.io
Resources
Readme
License
Activity
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0 watching
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0 forks
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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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pyranges
Coverage Statushypothesis testedPyPI versionMITPyPI - Python Versioninstall with bioconda
Introduction
PyRanges is a Python library specifically designed for efficient and intuitive manipulation of genomics data,
particularly genomic intervals (like genes, genomic features, or reads).
The library is optimized for fast querying and manipulation of genomic annotations.
"Finally ... This was what Python badly needed for years." - Heng Li
Documentation
The pyranges documentation is centralized at https://pyranges.readthedocs.io/
Visit it to find installation instructions, API, tutorial, and how-to-pages.
Features
  • fast
  • memory-efficient
  • featureful
  • pythonic/pandastic
  • supports chaining with a terse syntax
  • uses Pandas DataFrames, so the whole Python data science stack works on PyRanges.
Paper/Cite
Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36(3):918-919http://dx.doi.org/10.1093/bioinformatics/btz615
Supporting pyranges
  • most importantly, cite pyranges if you use it. It is the main metric funding sources care about.
  • use pyranges in Stack Overflow/biostars questions and answers
  • star the repo (possibly important for github visibility and as a proxy for project popularity)
  • if you are a business using pyranges, please give to one of the charities listed at https://www.givewell.org/
About
Performant Pythonic GenomicRanges
pyranges.readthedocs.io
Resources
Readme
License
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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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('^' + ".*" + '

Skip to content
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pyranges
Coverage Statushypothesis testedPyPI versionMITPyPI - Python Versioninstall with bioconda
Introduction
PyRanges is a Python library specifically designed for efficient and intuitive manipulation of genomics data,
particularly genomic intervals (like genes, genomic features, or reads).
The library is optimized for fast querying and manipulation of genomic annotations.
"Finally ... This was what Python badly needed for years." - Heng Li
Documentation
The pyranges documentation is centralized at https://pyranges.readthedocs.io/
Visit it to find installation instructions, API, tutorial, and how-to-pages.
Features
  • fast
  • memory-efficient
  • featureful
  • pythonic/pandastic
  • supports chaining with a terse syntax
  • uses Pandas DataFrames, so the whole Python data science stack works on PyRanges.
Paper/Cite
Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36(3):918-919http://dx.doi.org/10.1093/bioinformatics/btz615
Supporting pyranges
  • most importantly, cite pyranges if you use it. It is the main metric funding sources care about.
  • use pyranges in Stack Overflow/biostars questions and answers
  • star the repo (possibly important for github visibility and as a proxy for project popularity)
  • if you are a business using pyranges, please give to one of the charities listed at https://www.givewell.org/
About
Performant Pythonic GenomicRanges
pyranges.readthedocs.io
Resources
Readme
License
Activity
Custom properties
Stars
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0 watching
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0 forks
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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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pyranges
Coverage Statushypothesis testedPyPI versionMITPyPI - Python Versioninstall with bioconda
Introduction
PyRanges is a Python library specifically designed for efficient and intuitive manipulation of genomics data,
particularly genomic intervals (like genes, genomic features, or reads).
The library is optimized for fast querying and manipulation of genomic annotations.
"Finally ... This was what Python badly needed for years." - Heng Li
Documentation
The pyranges documentation is centralized at https://pyranges.readthedocs.io/
Visit it to find installation instructions, API, tutorial, and how-to-pages.
Features
  • fast
  • memory-efficient
  • featureful
  • pythonic/pandastic
  • supports chaining with a terse syntax
  • uses Pandas DataFrames, so the whole Python data science stack works on PyRanges.
Paper/Cite
Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36(3):918-919http://dx.doi.org/10.1093/bioinformatics/btz615
Supporting pyranges
  • most importantly, cite pyranges if you use it. It is the main metric funding sources care about.
  • use pyranges in Stack Overflow/biostars questions and answers
  • star the repo (possibly important for github visibility and as a proxy for project popularity)
  • if you are a business using pyranges, please give to one of the charities listed at https://www.givewell.org/
About
Performant Pythonic GenomicRanges
pyranges.readthedocs.io
Resources
Readme
License
Activity
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Stars
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0 watching
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