Skip to content
BranchesTags

Repository files navigation

GEMSTAT

This code implements the method from the paper

  • Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
  • Author: Xin He xinhe2@illinois.edu

Authors

See the file AUTHORS for information about additional authors and maintainers of this software.

Documentation

See the file named README.txt for documentation about building and running the program.

building

After checking out the repo, do:

git submodule init
git submodule update --recursive
mkdir build
cd build
cmake ..
make

Maintainers

See the file named MAINTAINER_README for more hints on how to maintain this software.

Builds

See Travis-Ci for continuous integration.

  • 'master':
  • 'develop':
  • 'bleeding-edge':

About

Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression

Resources

Readme
Activity
Custom properties

Stars

6 stars

Watchers

2 watching

Forks

8 forks
Report repository

Releases

Packages

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
 blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
GitHub - UIUCSinhaLab/GEMSTAT: Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression · GitHub
Skip to content
BranchesTags
Repository files navigation
GEMSTAT
This code implements the method from the paper
  • Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
  • Author: Xin He xinhe2@illinois.edu
Authors
See the file AUTHORS for information about additional authors and maintainers of this software.
Documentation
See the file named README.txt for documentation about building and running the program.
building
After checking out the repo, do:
git submodule init
git submodule update --recursive
mkdir build
cd build
cmake ..
make
Maintainers
See the file named MAINTAINER_README for more hints on how to maintain this software.
Builds
See Travis-Ci for continuous integration.
  • 'master': 
  • 'develop': 
  • 'bleeding-edge': 
About
Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
Resources
Readme
Activity
Custom properties
Stars
6 stars
Watchers
2 watching
Forks
8 forks
Report repository
Releases
Packages
Contributors
Languages

, '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 - UIUCSinhaLab/GEMSTAT: Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression · GitHub
Skip to content
BranchesTags
Repository files navigation
GEMSTAT
This code implements the method from the paper
  • Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
  • Author: Xin He xinhe2@illinois.edu
Authors
See the file AUTHORS for information about additional authors and maintainers of this software.
Documentation
See the file named README.txt for documentation about building and running the program.
building
After checking out the repo, do:
git submodule init
git submodule update --recursive
mkdir build
cd build
cmake ..
make
Maintainers
See the file named MAINTAINER_README for more hints on how to maintain this software.
Builds
See Travis-Ci for continuous integration.
  • 'master': 
  • 'develop': 
  • 'bleeding-edge': 
About
Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
Resources
Readme
Activity
Custom properties
Stars
6 stars
Watchers
2 watching
Forks
8 forks
Report repository
Releases
Packages
Contributors
Languages

, '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 - UIUCSinhaLab/GEMSTAT: Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression · GitHub
Skip to content
BranchesTags
Repository files navigation
GEMSTAT
This code implements the method from the paper
  • Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
  • Author: Xin He xinhe2@illinois.edu
Authors
See the file AUTHORS for information about additional authors and maintainers of this software.
Documentation
See the file named README.txt for documentation about building and running the program.
building
After checking out the repo, do:
git submodule init
git submodule update --recursive
mkdir build
cd build
cmake ..
make
Maintainers
See the file named MAINTAINER_README for more hints on how to maintain this software.
Builds
See Travis-Ci for continuous integration.
  • 'master': 
  • 'develop': 
  • 'bleeding-edge': 
About
Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
Resources
Readme
Activity
Custom properties
Stars
6 stars
Watchers
2 watching
Forks
8 forks
Report repository
Releases
Packages
Contributors
Languages

, '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 - UIUCSinhaLab/GEMSTAT: Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression · GitHub
Skip to content
BranchesTags
Repository files navigation
GEMSTAT
This code implements the method from the paper
  • Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
  • Author: Xin He xinhe2@illinois.edu
Authors
See the file AUTHORS for information about additional authors and maintainers of this software.
Documentation
See the file named README.txt for documentation about building and running the program.
building
After checking out the repo, do:
git submodule init
git submodule update --recursive
mkdir build
cd build
cmake ..
make
Maintainers
See the file named MAINTAINER_README for more hints on how to maintain this software.
Builds
See Travis-Ci for continuous integration.
  • 'master': 
  • 'develop': 
  • 'bleeding-edge': 
About
Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
Resources
Readme
Activity
Custom properties
Stars
6 stars
Watchers
2 watching
Forks
8 forks
Report repository
Releases
Packages
Contributors
Languages

, '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 - UIUCSinhaLab/GEMSTAT: Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression · GitHub
Skip to content
BranchesTags
Repository files navigation
GEMSTAT
This code implements the method from the paper
  • Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
  • Author: Xin He xinhe2@illinois.edu
Authors
See the file AUTHORS for information about additional authors and maintainers of this software.
Documentation
See the file named README.txt for documentation about building and running the program.
building
After checking out the repo, do:
git submodule init
git submodule update --recursive
mkdir build
cd build
cmake ..
make
Maintainers
See the file named MAINTAINER_README for more hints on how to maintain this software.
Builds
See Travis-Ci for continuous integration.
  • 'master': 
  • 'develop': 
  • 'bleeding-edge': 
About
Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
Resources
Readme
Activity
Custom properties
Stars
6 stars
Watchers
2 watching
Forks
8 forks
Report repository
Releases
Packages
Contributors
Languages

, '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 - UIUCSinhaLab/GEMSTAT: Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression · GitHub
Skip to content
BranchesTags
Repository files navigation
GEMSTAT
This code implements the method from the paper
  • Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
  • Author: Xin He xinhe2@illinois.edu
Authors
See the file AUTHORS for information about additional authors and maintainers of this software.
Documentation
See the file named README.txt for documentation about building and running the program.
building
After checking out the repo, do:
git submodule init
git submodule update --recursive
mkdir build
cd build
cmake ..
make
Maintainers
See the file named MAINTAINER_README for more hints on how to maintain this software.
Builds
See Travis-Ci for continuous integration.
  • 'master': 
  • 'develop': 
  • 'bleeding-edge': 
About
Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
Resources
Readme
Activity
Custom properties
Stars
6 stars
Watchers
2 watching
Forks
8 forks
Report repository
Releases
Packages
Contributors
Languages

, '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 - UIUCSinhaLab/GEMSTAT: Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression · GitHub
Skip to content
BranchesTags
Repository files navigation
GEMSTAT
This code implements the method from the paper
  • Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
  • Author: Xin He xinhe2@illinois.edu
Authors
See the file AUTHORS for information about additional authors and maintainers of this software.
Documentation
See the file named README.txt for documentation about building and running the program.
building
After checking out the repo, do:
git submodule init
git submodule update --recursive
mkdir build
cd build
cmake ..
make
Maintainers
See the file named MAINTAINER_README for more hints on how to maintain this software.
Builds
See Travis-Ci for continuous integration.
  • 'master': 
  • 'develop': 
  • 'bleeding-edge': 
About
Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
Resources
Readme
Activity
Custom properties
Stars
6 stars
Watchers
2 watching
Forks
8 forks
Report repository
Releases
Packages
Contributors
Languages