BranchesTags

Repository files navigation

PathwayEmbed

We are focusing on estimating intracellular signal transduction states vis distance embedding

PathwayEmbed

Build StatusLicense: MIT

PathwayEmbed is an R package for quantifying and visualizing intracellular signaling pathway activation from transcriptomic data, integrating pathway topology and gene expression data.

Installation

You can install the released version of PathwayEmbed from GitHub using:

# Install remotes if you haven't alreadyif (!requireNamespace("remotes", quietly=TRUE)) {
install.packages("remotes")
}
remotes::install_github("RaredonLab/PathwayEmbed")

Usage

library(PathwayEmbed)
# Load example data included with the package
data("synthetic_test_object_100")
data("synthetic_test_metadata")
# Check what pathways are availabel in the pre-constructed table
ListPathway() # summary page
ListPathway("Pathway") # what pathways are available
ListPathway("WNT") # what coefficient tables are available# Load pre-constructed pathway coefficient tablesWnt_12h<- LoadPathway("WNT3A_12H_ACTIVATION", "mouse")
# Input data preprocess matrix_12h<- DataPreProcess(synthetic_test_object_100, Wnt_12h, Seurat.object=TRUE)
# Determine the global reference (ON and OFF)pathwaystat_12h<- PathwayMaxMin(matrix_12h, Wnt_12h)
# Compute pathway datascore_12h<- ComputeCellData(matrix_12h, pathwaystat_12h)
# Prepare data for plottingplot_data_12h<- PreparePlotData(synthetic_test_metadata, score_12h, group="genotype")
# Plot pathway activation
PlotPathway(plot_data_12h, "12hr Wnt", "genotype", c("#ae282c", "#2066a8"))
# Calculate percentage and do comparison between two groups (optional)
CalculatePercentage(to.plot=plot_data_12h, group_var="genotype")

About

No description, website, or topics provided.

Resources

Readme
Activity

Stars

0 stars

Watchers

1 watching

Forks

1 fork
Report repository

Releases

Packages

Contributors

Languages

, '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
PathwayEmbed
We are focusing on estimating intracellular signal transduction states vis distance embedding
PathwayEmbed
Build StatusLicense: MIT
PathwayEmbed is an R package for quantifying and visualizing intracellular signaling pathway activation from transcriptomic data, integrating pathway topology and gene expression data.
Installation
You can install the released version of PathwayEmbed from GitHub using:
# Install remotes if you haven't alreadyif (!requireNamespace("remotes", quietly=TRUE)) {
install.packages("remotes")
}
remotes::install_github("RaredonLab/PathwayEmbed")

Usage
library(PathwayEmbed)
# Load example data included with the package
data("synthetic_test_object_100")
data("synthetic_test_metadata")
# Check what pathways are availabel in the pre-constructed table
ListPathway() # summary page
ListPathway("Pathway") # what pathways are available
ListPathway("WNT") # what coefficient tables are available# Load pre-constructed pathway coefficient tablesWnt_12h<- LoadPathway("WNT3A_12H_ACTIVATION", "mouse")
# Input data preprocess matrix_12h<- DataPreProcess(synthetic_test_object_100, Wnt_12h, Seurat.object=TRUE)
# Determine the global reference (ON and OFF)pathwaystat_12h<- PathwayMaxMin(matrix_12h, Wnt_12h)
# Compute pathway datascore_12h<- ComputeCellData(matrix_12h, pathwaystat_12h)
# Prepare data for plottingplot_data_12h<- PreparePlotData(synthetic_test_metadata, score_12h, group="genotype")
# Plot pathway activation
PlotPathway(plot_data_12h, "12hr Wnt", "genotype", c("#ae282c", "#2066a8"))
# Calculate percentage and do comparison between two groups (optional)
CalculatePercentage(to.plot=plot_data_12h, group_var="genotype")

About
No description, website, or topics provided.
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, '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
PathwayEmbed
We are focusing on estimating intracellular signal transduction states vis distance embedding
PathwayEmbed
Build StatusLicense: MIT
PathwayEmbed is an R package for quantifying and visualizing intracellular signaling pathway activation from transcriptomic data, integrating pathway topology and gene expression data.
Installation
You can install the released version of PathwayEmbed from GitHub using:
# Install remotes if you haven't alreadyif (!requireNamespace("remotes", quietly=TRUE)) {
install.packages("remotes")
}
remotes::install_github("RaredonLab/PathwayEmbed")

Usage
library(PathwayEmbed)
# Load example data included with the package
data("synthetic_test_object_100")
data("synthetic_test_metadata")
# Check what pathways are availabel in the pre-constructed table
ListPathway() # summary page
ListPathway("Pathway") # what pathways are available
ListPathway("WNT") # what coefficient tables are available# Load pre-constructed pathway coefficient tablesWnt_12h<- LoadPathway("WNT3A_12H_ACTIVATION", "mouse")
# Input data preprocess matrix_12h<- DataPreProcess(synthetic_test_object_100, Wnt_12h, Seurat.object=TRUE)
# Determine the global reference (ON and OFF)pathwaystat_12h<- PathwayMaxMin(matrix_12h, Wnt_12h)
# Compute pathway datascore_12h<- ComputeCellData(matrix_12h, pathwaystat_12h)
# Prepare data for plottingplot_data_12h<- PreparePlotData(synthetic_test_metadata, score_12h, group="genotype")
# Plot pathway activation
PlotPathway(plot_data_12h, "12hr Wnt", "genotype", c("#ae282c", "#2066a8"))
# Calculate percentage and do comparison between two groups (optional)
CalculatePercentage(to.plot=plot_data_12h, group_var="genotype")

About
No description, website, or topics provided.
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, '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
PathwayEmbed
We are focusing on estimating intracellular signal transduction states vis distance embedding
PathwayEmbed
Build StatusLicense: MIT
PathwayEmbed is an R package for quantifying and visualizing intracellular signaling pathway activation from transcriptomic data, integrating pathway topology and gene expression data.
Installation
You can install the released version of PathwayEmbed from GitHub using:
# Install remotes if you haven't alreadyif (!requireNamespace("remotes", quietly=TRUE)) {
install.packages("remotes")
}
remotes::install_github("RaredonLab/PathwayEmbed")

Usage
library(PathwayEmbed)
# Load example data included with the package
data("synthetic_test_object_100")
data("synthetic_test_metadata")
# Check what pathways are availabel in the pre-constructed table
ListPathway() # summary page
ListPathway("Pathway") # what pathways are available
ListPathway("WNT") # what coefficient tables are available# Load pre-constructed pathway coefficient tablesWnt_12h<- LoadPathway("WNT3A_12H_ACTIVATION", "mouse")
# Input data preprocess matrix_12h<- DataPreProcess(synthetic_test_object_100, Wnt_12h, Seurat.object=TRUE)
# Determine the global reference (ON and OFF)pathwaystat_12h<- PathwayMaxMin(matrix_12h, Wnt_12h)
# Compute pathway datascore_12h<- ComputeCellData(matrix_12h, pathwaystat_12h)
# Prepare data for plottingplot_data_12h<- PreparePlotData(synthetic_test_metadata, score_12h, group="genotype")
# Plot pathway activation
PlotPathway(plot_data_12h, "12hr Wnt", "genotype", c("#ae282c", "#2066a8"))
# Calculate percentage and do comparison between two groups (optional)
CalculatePercentage(to.plot=plot_data_12h, group_var="genotype")

About
No description, website, or topics provided.
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, '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
PathwayEmbed
We are focusing on estimating intracellular signal transduction states vis distance embedding
PathwayEmbed
Build StatusLicense: MIT
PathwayEmbed is an R package for quantifying and visualizing intracellular signaling pathway activation from transcriptomic data, integrating pathway topology and gene expression data.
Installation
You can install the released version of PathwayEmbed from GitHub using:
# Install remotes if you haven't alreadyif (!requireNamespace("remotes", quietly=TRUE)) {
install.packages("remotes")
}
remotes::install_github("RaredonLab/PathwayEmbed")

Usage
library(PathwayEmbed)
# Load example data included with the package
data("synthetic_test_object_100")
data("synthetic_test_metadata")
# Check what pathways are availabel in the pre-constructed table
ListPathway() # summary page
ListPathway("Pathway") # what pathways are available
ListPathway("WNT") # what coefficient tables are available# Load pre-constructed pathway coefficient tablesWnt_12h<- LoadPathway("WNT3A_12H_ACTIVATION", "mouse")
# Input data preprocess matrix_12h<- DataPreProcess(synthetic_test_object_100, Wnt_12h, Seurat.object=TRUE)
# Determine the global reference (ON and OFF)pathwaystat_12h<- PathwayMaxMin(matrix_12h, Wnt_12h)
# Compute pathway datascore_12h<- ComputeCellData(matrix_12h, pathwaystat_12h)
# Prepare data for plottingplot_data_12h<- PreparePlotData(synthetic_test_metadata, score_12h, group="genotype")
# Plot pathway activation
PlotPathway(plot_data_12h, "12hr Wnt", "genotype", c("#ae282c", "#2066a8"))
# Calculate percentage and do comparison between two groups (optional)
CalculatePercentage(to.plot=plot_data_12h, group_var="genotype")

About
No description, website, or topics provided.
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, '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
PathwayEmbed
We are focusing on estimating intracellular signal transduction states vis distance embedding
PathwayEmbed
Build StatusLicense: MIT
PathwayEmbed is an R package for quantifying and visualizing intracellular signaling pathway activation from transcriptomic data, integrating pathway topology and gene expression data.
Installation
You can install the released version of PathwayEmbed from GitHub using:
# Install remotes if you haven't alreadyif (!requireNamespace("remotes", quietly=TRUE)) {
install.packages("remotes")
}
remotes::install_github("RaredonLab/PathwayEmbed")

Usage
library(PathwayEmbed)
# Load example data included with the package
data("synthetic_test_object_100")
data("synthetic_test_metadata")
# Check what pathways are availabel in the pre-constructed table
ListPathway() # summary page
ListPathway("Pathway") # what pathways are available
ListPathway("WNT") # what coefficient tables are available# Load pre-constructed pathway coefficient tablesWnt_12h<- LoadPathway("WNT3A_12H_ACTIVATION", "mouse")
# Input data preprocess matrix_12h<- DataPreProcess(synthetic_test_object_100, Wnt_12h, Seurat.object=TRUE)
# Determine the global reference (ON and OFF)pathwaystat_12h<- PathwayMaxMin(matrix_12h, Wnt_12h)
# Compute pathway datascore_12h<- ComputeCellData(matrix_12h, pathwaystat_12h)
# Prepare data for plottingplot_data_12h<- PreparePlotData(synthetic_test_metadata, score_12h, group="genotype")
# Plot pathway activation
PlotPathway(plot_data_12h, "12hr Wnt", "genotype", c("#ae282c", "#2066a8"))
# Calculate percentage and do comparison between two groups (optional)
CalculatePercentage(to.plot=plot_data_12h, group_var="genotype")

About
No description, website, or topics provided.
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, '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
PathwayEmbed
We are focusing on estimating intracellular signal transduction states vis distance embedding
PathwayEmbed
Build StatusLicense: MIT
PathwayEmbed is an R package for quantifying and visualizing intracellular signaling pathway activation from transcriptomic data, integrating pathway topology and gene expression data.
Installation
You can install the released version of PathwayEmbed from GitHub using:
# Install remotes if you haven't alreadyif (!requireNamespace("remotes", quietly=TRUE)) {
install.packages("remotes")
}
remotes::install_github("RaredonLab/PathwayEmbed")

Usage
library(PathwayEmbed)
# Load example data included with the package
data("synthetic_test_object_100")
data("synthetic_test_metadata")
# Check what pathways are availabel in the pre-constructed table
ListPathway() # summary page
ListPathway("Pathway") # what pathways are available
ListPathway("WNT") # what coefficient tables are available# Load pre-constructed pathway coefficient tablesWnt_12h<- LoadPathway("WNT3A_12H_ACTIVATION", "mouse")
# Input data preprocess matrix_12h<- DataPreProcess(synthetic_test_object_100, Wnt_12h, Seurat.object=TRUE)
# Determine the global reference (ON and OFF)pathwaystat_12h<- PathwayMaxMin(matrix_12h, Wnt_12h)
# Compute pathway datascore_12h<- ComputeCellData(matrix_12h, pathwaystat_12h)
# Prepare data for plottingplot_data_12h<- PreparePlotData(synthetic_test_metadata, score_12h, group="genotype")
# Plot pathway activation
PlotPathway(plot_data_12h, "12hr Wnt", "genotype", c("#ae282c", "#2066a8"))
# Calculate percentage and do comparison between two groups (optional)
CalculatePercentage(to.plot=plot_data_12h, group_var="genotype")

About
No description, website, or topics provided.
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, '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
BranchesTags
Repository files navigation
PathwayEmbed
We are focusing on estimating intracellular signal transduction states vis distance embedding
PathwayEmbed
Build StatusLicense: MIT
PathwayEmbed is an R package for quantifying and visualizing intracellular signaling pathway activation from transcriptomic data, integrating pathway topology and gene expression data.
Installation
You can install the released version of PathwayEmbed from GitHub using:
# Install remotes if you haven't alreadyif (!requireNamespace("remotes", quietly=TRUE)) {
install.packages("remotes")
}
remotes::install_github("RaredonLab/PathwayEmbed")

Usage
library(PathwayEmbed)
# Load example data included with the package
data("synthetic_test_object_100")
data("synthetic_test_metadata")
# Check what pathways are availabel in the pre-constructed table
ListPathway() # summary page
ListPathway("Pathway") # what pathways are available
ListPathway("WNT") # what coefficient tables are available# Load pre-constructed pathway coefficient tablesWnt_12h<- LoadPathway("WNT3A_12H_ACTIVATION", "mouse")
# Input data preprocess matrix_12h<- DataPreProcess(synthetic_test_object_100, Wnt_12h, Seurat.object=TRUE)
# Determine the global reference (ON and OFF)pathwaystat_12h<- PathwayMaxMin(matrix_12h, Wnt_12h)
# Compute pathway datascore_12h<- ComputeCellData(matrix_12h, pathwaystat_12h)
# Prepare data for plottingplot_data_12h<- PreparePlotData(synthetic_test_metadata, score_12h, group="genotype")
# Plot pathway activation
PlotPathway(plot_data_12h, "12hr Wnt", "genotype", c("#ae282c", "#2066a8"))
# Calculate percentage and do comparison between two groups (optional)
CalculatePercentage(to.plot=plot_data_12h, group_var="genotype")

About
No description, website, or topics provided.
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages