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Data Analysis for Genomics

NEWS:

May 7, 2014: in order to clean up and trim down the memory size of this repo, we've moved out non-code objects out of this repo. Therefore, before submitting a pull request, please first clone a clean copy of the repository. The celfiles and agilent folder of week2 has been moved to the rawdata repo, and the reading microarray lab has been updated to reflect this.

May 5, 2014 : we are adding rendered content here: http://genomicsclass.github.io/book/

Labs and lectures:

Week 1: Introduction

  • What we measure and why
  • R programming skills
  • Probability distributions
  • Exploratory data analysis

Week 2: Measurement technology

  • Microarray technology
  • Next generation sequencing technology
  • Working with data in R

Week 3: Inference

  • Inference
  • Linear models

Week 4: Background correction and normalization

  • Modeling
  • Background
  • Normalization

Week 5: Distance, clustering, and prediction

  • Distance and clustering
  • Prediction

Week 6: Batch effects

  • Statistical solutions to batch effects
  • Applying batch effects solutions

Week 7: Advanced differential expression

  • Hierarchical modeling
  • Multiple comparisons
  • Gene set testing
  • Gene and technology annotations

Week 8: Advanced topics

  • Manipulating NGS data using Bioconductor
  • Genome variation
  • RNA sequencing
  • DNA methylation
  • ChIP sequencing

About

Scripts for PH525x: Data Analysis for Genomics

www.edx.org/course/harvardx/harvardx-ph525x-data-analysis-genomics-1401

Resources

Readme
MIT license
Activity

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Watchers

1 watching

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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
BranchesTags
Repository files navigation
Data Analysis for Genomics
NEWS:
May 7, 2014: in order to clean up and trim down the memory size of
this repo, we've moved out non-code objects
out of this repo. Therefore, before submitting a pull request,
please first clone a clean copy of the repository.
The celfiles and agilent folder of week2 has been
moved to the rawdata repo, and the reading microarray lab has
been updated to reflect this.
May 5, 2014 : we are adding rendered content here: http://genomicsclass.github.io/book/
Labs and lectures:
Week 1: Introduction
  • What we measure and why
  • R programming skills
  • Probability distributions
  • Exploratory data analysis
Week 2: Measurement technology
  • Microarray technology
  • Next generation sequencing technology
  • Working with data in R
Week 3: Inference
  • Inference
  • Linear models
Week 4: Background correction and normalization
  • Modeling
  • Background
  • Normalization
Week 5: Distance, clustering, and prediction
  • Distance and clustering
  • Prediction
Week 6: Batch effects
  • Statistical solutions to batch effects
  • Applying batch effects solutions
Week 7: Advanced differential expression
  • Hierarchical modeling
  • Multiple comparisons
  • Gene set testing
  • Gene and technology annotations
Week 8: Advanced topics
  • Manipulating NGS data using Bioconductor
  • Genome variation
  • RNA sequencing
  • DNA methylation
  • ChIP sequencing
About
Scripts for PH525x: Data Analysis for Genomics
www.edx.org/course/harvardx/harvardx-ph525x-data-analysis-genomics-1401
Resources
Readme
MIT license
Activity
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1 watching
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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
BranchesTags
Repository files navigation
Data Analysis for Genomics
NEWS:
May 7, 2014: in order to clean up and trim down the memory size of
this repo, we've moved out non-code objects
out of this repo. Therefore, before submitting a pull request,
please first clone a clean copy of the repository.
The celfiles and agilent folder of week2 has been
moved to the rawdata repo, and the reading microarray lab has
been updated to reflect this.
May 5, 2014 : we are adding rendered content here: http://genomicsclass.github.io/book/
Labs and lectures:
Week 1: Introduction
  • What we measure and why
  • R programming skills
  • Probability distributions
  • Exploratory data analysis
Week 2: Measurement technology
  • Microarray technology
  • Next generation sequencing technology
  • Working with data in R
Week 3: Inference
  • Inference
  • Linear models
Week 4: Background correction and normalization
  • Modeling
  • Background
  • Normalization
Week 5: Distance, clustering, and prediction
  • Distance and clustering
  • Prediction
Week 6: Batch effects
  • Statistical solutions to batch effects
  • Applying batch effects solutions
Week 7: Advanced differential expression
  • Hierarchical modeling
  • Multiple comparisons
  • Gene set testing
  • Gene and technology annotations
Week 8: Advanced topics
  • Manipulating NGS data using Bioconductor
  • Genome variation
  • RNA sequencing
  • DNA methylation
  • ChIP sequencing
About
Scripts for PH525x: Data Analysis for Genomics
www.edx.org/course/harvardx/harvardx-ph525x-data-analysis-genomics-1401
Resources
Readme
MIT license
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
Data Analysis for Genomics
NEWS:
May 7, 2014: in order to clean up and trim down the memory size of
this repo, we've moved out non-code objects
out of this repo. Therefore, before submitting a pull request,
please first clone a clean copy of the repository.
The celfiles and agilent folder of week2 has been
moved to the rawdata repo, and the reading microarray lab has
been updated to reflect this.
May 5, 2014 : we are adding rendered content here: http://genomicsclass.github.io/book/
Labs and lectures:
Week 1: Introduction
  • What we measure and why
  • R programming skills
  • Probability distributions
  • Exploratory data analysis
Week 2: Measurement technology
  • Microarray technology
  • Next generation sequencing technology
  • Working with data in R
Week 3: Inference
  • Inference
  • Linear models
Week 4: Background correction and normalization
  • Modeling
  • Background
  • Normalization
Week 5: Distance, clustering, and prediction
  • Distance and clustering
  • Prediction
Week 6: Batch effects
  • Statistical solutions to batch effects
  • Applying batch effects solutions
Week 7: Advanced differential expression
  • Hierarchical modeling
  • Multiple comparisons
  • Gene set testing
  • Gene and technology annotations
Week 8: Advanced topics
  • Manipulating NGS data using Bioconductor
  • Genome variation
  • RNA sequencing
  • DNA methylation
  • ChIP sequencing
About
Scripts for PH525x: Data Analysis for Genomics
www.edx.org/course/harvardx/harvardx-ph525x-data-analysis-genomics-1401
Resources
Readme
MIT license
Activity
Stars
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1 watching
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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
Repository files navigation
Data Analysis for Genomics
NEWS:
May 7, 2014: in order to clean up and trim down the memory size of
this repo, we've moved out non-code objects
out of this repo. Therefore, before submitting a pull request,
please first clone a clean copy of the repository.
The celfiles and agilent folder of week2 has been
moved to the rawdata repo, and the reading microarray lab has
been updated to reflect this.
May 5, 2014 : we are adding rendered content here: http://genomicsclass.github.io/book/
Labs and lectures:
Week 1: Introduction
  • What we measure and why
  • R programming skills
  • Probability distributions
  • Exploratory data analysis
Week 2: Measurement technology
  • Microarray technology
  • Next generation sequencing technology
  • Working with data in R
Week 3: Inference
  • Inference
  • Linear models
Week 4: Background correction and normalization
  • Modeling
  • Background
  • Normalization
Week 5: Distance, clustering, and prediction
  • Distance and clustering
  • Prediction
Week 6: Batch effects
  • Statistical solutions to batch effects
  • Applying batch effects solutions
Week 7: Advanced differential expression
  • Hierarchical modeling
  • Multiple comparisons
  • Gene set testing
  • Gene and technology annotations
Week 8: Advanced topics
  • Manipulating NGS data using Bioconductor
  • Genome variation
  • RNA sequencing
  • DNA methylation
  • ChIP sequencing
About
Scripts for PH525x: Data Analysis for Genomics
www.edx.org/course/harvardx/harvardx-ph525x-data-analysis-genomics-1401
Resources
Readme
MIT license
Activity
Stars
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Watchers
1 watching
Forks
0 forks
Report repository
Releases
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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
Data Analysis for Genomics
NEWS:
May 7, 2014: in order to clean up and trim down the memory size of
this repo, we've moved out non-code objects
out of this repo. Therefore, before submitting a pull request,
please first clone a clean copy of the repository.
The celfiles and agilent folder of week2 has been
moved to the rawdata repo, and the reading microarray lab has
been updated to reflect this.
May 5, 2014 : we are adding rendered content here: http://genomicsclass.github.io/book/
Labs and lectures:
Week 1: Introduction
  • What we measure and why
  • R programming skills
  • Probability distributions
  • Exploratory data analysis
Week 2: Measurement technology
  • Microarray technology
  • Next generation sequencing technology
  • Working with data in R
Week 3: Inference
  • Inference
  • Linear models
Week 4: Background correction and normalization
  • Modeling
  • Background
  • Normalization
Week 5: Distance, clustering, and prediction
  • Distance and clustering
  • Prediction
Week 6: Batch effects
  • Statistical solutions to batch effects
  • Applying batch effects solutions
Week 7: Advanced differential expression
  • Hierarchical modeling
  • Multiple comparisons
  • Gene set testing
  • Gene and technology annotations
Week 8: Advanced topics
  • Manipulating NGS data using Bioconductor
  • Genome variation
  • RNA sequencing
  • DNA methylation
  • ChIP sequencing
About
Scripts for PH525x: Data Analysis for Genomics
www.edx.org/course/harvardx/harvardx-ph525x-data-analysis-genomics-1401
Resources
Readme
MIT license
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
Data Analysis for Genomics
NEWS:
May 7, 2014: in order to clean up and trim down the memory size of
this repo, we've moved out non-code objects
out of this repo. Therefore, before submitting a pull request,
please first clone a clean copy of the repository.
The celfiles and agilent folder of week2 has been
moved to the rawdata repo, and the reading microarray lab has
been updated to reflect this.
May 5, 2014 : we are adding rendered content here: http://genomicsclass.github.io/book/
Labs and lectures:
Week 1: Introduction
  • What we measure and why
  • R programming skills
  • Probability distributions
  • Exploratory data analysis
Week 2: Measurement technology
  • Microarray technology
  • Next generation sequencing technology
  • Working with data in R
Week 3: Inference
  • Inference
  • Linear models
Week 4: Background correction and normalization
  • Modeling
  • Background
  • Normalization
Week 5: Distance, clustering, and prediction
  • Distance and clustering
  • Prediction
Week 6: Batch effects
  • Statistical solutions to batch effects
  • Applying batch effects solutions
Week 7: Advanced differential expression
  • Hierarchical modeling
  • Multiple comparisons
  • Gene set testing
  • Gene and technology annotations
Week 8: Advanced topics
  • Manipulating NGS data using Bioconductor
  • Genome variation
  • RNA sequencing
  • DNA methylation
  • ChIP sequencing
About
Scripts for PH525x: Data Analysis for Genomics
www.edx.org/course/harvardx/harvardx-ph525x-data-analysis-genomics-1401
Resources
Readme
MIT license
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); }
})();
})();

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Data Analysis for Genomics
NEWS:
May 7, 2014: in order to clean up and trim down the memory size of
this repo, we've moved out non-code objects
out of this repo. Therefore, before submitting a pull request,
please first clone a clean copy of the repository.
The celfiles and agilent folder of week2 has been
moved to the rawdata repo, and the reading microarray lab has
been updated to reflect this.
May 5, 2014 : we are adding rendered content here: http://genomicsclass.github.io/book/
Labs and lectures:
Week 1: Introduction
  • What we measure and why
  • R programming skills
  • Probability distributions
  • Exploratory data analysis
Week 2: Measurement technology
  • Microarray technology
  • Next generation sequencing technology
  • Working with data in R
Week 3: Inference
  • Inference
  • Linear models
Week 4: Background correction and normalization
  • Modeling
  • Background
  • Normalization
Week 5: Distance, clustering, and prediction
  • Distance and clustering
  • Prediction
Week 6: Batch effects
  • Statistical solutions to batch effects
  • Applying batch effects solutions
Week 7: Advanced differential expression
  • Hierarchical modeling
  • Multiple comparisons
  • Gene set testing
  • Gene and technology annotations
Week 8: Advanced topics
  • Manipulating NGS data using Bioconductor
  • Genome variation
  • RNA sequencing
  • DNA methylation
  • ChIP sequencing
About
Scripts for PH525x: Data Analysis for Genomics
www.edx.org/course/harvardx/harvardx-ph525x-data-analysis-genomics-1401
Resources
Readme
MIT license
Activity
Stars
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Watchers
1 watching
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Report repository
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Contributors