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Reproducible Research

This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.

The goal is to build a directory of useful links, and a jargon busting glossary.

Table of contents

Click on the links below to go straight to the following resources:

Guide for contributors

See our guidelines for how to contribute to the project.

A good place to start is to build the Jargon Buster glossary. Pick a word you remember learning (preferably related to Reproducible Research but not necessarily), define it and submit a pull request so everyone else can learn with you!

Alternatively, you could add a resource to our Resources page. If there's a link you've found helpful, please add it to the list and submit a pull request to share with the community.

Code of conduct

Everyone is welcome to join this project, particularly people who have not used GitHub before and are feeling unsure of how to begin!

Please follow our code of conduct in all your on and offline interactions.

About

This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.

Resources

Readme

Code of conduct

Code of conduct

Contributing

Contributing
Activity
Custom properties

Stars

32 stars

Watchers

10 watching

Forks

16 forks
Report repository

Releases

Packages

Contributors

, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
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(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" + '
GitHub - WhitakerLab/ReproducibleResearch: This repository supports Kirstie's presentation on tips and tricks for making your research reproducible. · GitHub
Skip to content
BranchesTags
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Reproducible Research
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
The goal is to build a directory of useful links, and a jargon busting glossary.
Table of contents
Click on the links below to go straight to the following resources:
Guide for contributors
See our guidelines for how to contribute to the project.
A good place to start is to build the Jargon Buster glossary. Pick a word you remember learning (preferably related to Reproducible Research but not necessarily), define it and submit a pull request so everyone else can learn with you!
Alternatively, you could add a resource to our Resources page. If there's a link you've found helpful, please add it to the list and submit a pull request to share with the community.
Code of conduct
Everyone is welcome to join this project, particularly people who have not used GitHub before and are feeling unsure of how to begin!
Please follow our code of conduct in all your on and offline interactions.
About
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
Resources
Readme
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
32 stars
Watchers
10 watching
Forks
16 forks
Report repository
Releases
Packages
Contributors

, '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('^' + ".*" + '
GitHub - WhitakerLab/ReproducibleResearch: This repository supports Kirstie's presentation on tips and tricks for making your research reproducible. · GitHub
Skip to content
BranchesTags
Repository files navigation
Reproducible Research
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
The goal is to build a directory of useful links, and a jargon busting glossary.
Table of contents
Click on the links below to go straight to the following resources:
Guide for contributors
See our guidelines for how to contribute to the project.
A good place to start is to build the Jargon Buster glossary. Pick a word you remember learning (preferably related to Reproducible Research but not necessarily), define it and submit a pull request so everyone else can learn with you!
Alternatively, you could add a resource to our Resources page. If there's a link you've found helpful, please add it to the list and submit a pull request to share with the community.
Code of conduct
Everyone is welcome to join this project, particularly people who have not used GitHub before and are feeling unsure of how to begin!
Please follow our code of conduct in all your on and offline interactions.
About
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
Resources
Readme
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
32 stars
Watchers
10 watching
Forks
16 forks
Report repository
Releases
Packages
Contributors

, '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('^' + ".*" + '
GitHub - WhitakerLab/ReproducibleResearch: This repository supports Kirstie's presentation on tips and tricks for making your research reproducible. · GitHub
Skip to content
BranchesTags
Repository files navigation
Reproducible Research
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
The goal is to build a directory of useful links, and a jargon busting glossary.
Table of contents
Click on the links below to go straight to the following resources:
Guide for contributors
See our guidelines for how to contribute to the project.
A good place to start is to build the Jargon Buster glossary. Pick a word you remember learning (preferably related to Reproducible Research but not necessarily), define it and submit a pull request so everyone else can learn with you!
Alternatively, you could add a resource to our Resources page. If there's a link you've found helpful, please add it to the list and submit a pull request to share with the community.
Code of conduct
Everyone is welcome to join this project, particularly people who have not used GitHub before and are feeling unsure of how to begin!
Please follow our code of conduct in all your on and offline interactions.
About
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
Resources
Readme
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
32 stars
Watchers
10 watching
Forks
16 forks
Report repository
Releases
Packages
Contributors

, '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" + '
GitHub - WhitakerLab/ReproducibleResearch: This repository supports Kirstie's presentation on tips and tricks for making your research reproducible. · GitHub
Skip to content
BranchesTags
Repository files navigation
Reproducible Research
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
The goal is to build a directory of useful links, and a jargon busting glossary.
Table of contents
Click on the links below to go straight to the following resources:
Guide for contributors
See our guidelines for how to contribute to the project.
A good place to start is to build the Jargon Buster glossary. Pick a word you remember learning (preferably related to Reproducible Research but not necessarily), define it and submit a pull request so everyone else can learn with you!
Alternatively, you could add a resource to our Resources page. If there's a link you've found helpful, please add it to the list and submit a pull request to share with the community.
Code of conduct
Everyone is welcome to join this project, particularly people who have not used GitHub before and are feeling unsure of how to begin!
Please follow our code of conduct in all your on and offline interactions.
About
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
Resources
Readme
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
32 stars
Watchers
10 watching
Forks
16 forks
Report repository
Releases
Packages
Contributors

, '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('^' + ".*" + '
GitHub - WhitakerLab/ReproducibleResearch: This repository supports Kirstie's presentation on tips and tricks for making your research reproducible. · GitHub
Skip to content
BranchesTags
Repository files navigation
Reproducible Research
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
The goal is to build a directory of useful links, and a jargon busting glossary.
Table of contents
Click on the links below to go straight to the following resources:
Guide for contributors
See our guidelines for how to contribute to the project.
A good place to start is to build the Jargon Buster glossary. Pick a word you remember learning (preferably related to Reproducible Research but not necessarily), define it and submit a pull request so everyone else can learn with you!
Alternatively, you could add a resource to our Resources page. If there's a link you've found helpful, please add it to the list and submit a pull request to share with the community.
Code of conduct
Everyone is welcome to join this project, particularly people who have not used GitHub before and are feeling unsure of how to begin!
Please follow our code of conduct in all your on and offline interactions.
About
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
Resources
Readme
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
32 stars
Watchers
10 watching
Forks
16 forks
Report repository
Releases
Packages
Contributors

, '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('^' + ".*" + '
GitHub - WhitakerLab/ReproducibleResearch: This repository supports Kirstie's presentation on tips and tricks for making your research reproducible. · GitHub
Skip to content
BranchesTags
Repository files navigation
Reproducible Research
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
The goal is to build a directory of useful links, and a jargon busting glossary.
Table of contents
Click on the links below to go straight to the following resources:
Guide for contributors
See our guidelines for how to contribute to the project.
A good place to start is to build the Jargon Buster glossary. Pick a word you remember learning (preferably related to Reproducible Research but not necessarily), define it and submit a pull request so everyone else can learn with you!
Alternatively, you could add a resource to our Resources page. If there's a link you've found helpful, please add it to the list and submit a pull request to share with the community.
Code of conduct
Everyone is welcome to join this project, particularly people who have not used GitHub before and are feeling unsure of how to begin!
Please follow our code of conduct in all your on and offline interactions.
About
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
Resources
Readme
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
32 stars
Watchers
10 watching
Forks
16 forks
Report repository
Releases
Packages
Contributors

, '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); }
})();
})();
GitHub - WhitakerLab/ReproducibleResearch: This repository supports Kirstie's presentation on tips and tricks for making your research reproducible. · GitHub
Skip to content
BranchesTags
Repository files navigation
Reproducible Research
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
The goal is to build a directory of useful links, and a jargon busting glossary.
Table of contents
Click on the links below to go straight to the following resources:
Guide for contributors
See our guidelines for how to contribute to the project.
A good place to start is to build the Jargon Buster glossary. Pick a word you remember learning (preferably related to Reproducible Research but not necessarily), define it and submit a pull request so everyone else can learn with you!
Alternatively, you could add a resource to our Resources page. If there's a link you've found helpful, please add it to the list and submit a pull request to share with the community.
Code of conduct
Everyone is welcome to join this project, particularly people who have not used GitHub before and are feeling unsure of how to begin!
Please follow our code of conduct in all your on and offline interactions.
About
This repository supports Kirstie's presentation on tips and tricks for making your research reproducible.
Resources
Readme
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
32 stars
Watchers
10 watching
Forks
16 forks
Report repository
Releases
Packages
Contributors