Skip to content
BranchesTags

Repository files navigation

Build Status

RRVGO

Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.

Introduction to rrvgo

Gene Ontologies (GO) are often used to guide the interpretation of high-throughput omics experiments, with lists of differentially regulated genes being summarized into sets of genes with a common functional representation. Due to the hierachical nature of Gene Ontologies, the resulting lists of enriched sets are usually redundant and difficult to interpret.

rrvgo aims at simplifying the redundance of GO sets by grouping similar terms in terms of semantic similarity. It also provides some plots to help with interpreting the summarized terms.

This software is heavily influenced by REVIGO. It mimics a good part of its core functionality, and even some of the outputs are similar. Without aims to compete, rrvgo tries to offer a programatic interface using available annotation databases and semantic similarity methods implemented in the Bioconductor project.

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("rrvgo")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("rrvgo")

or access the pkgdown documentation.

Dependencies

Imports (mandatory for core functionality)

  • GOSemSim: Semantic similarity computation among GO terms.
  • AnnotationDbi: Provides user interface and database connection code for annotation data packages using SQLite data storage.
  • GO.db: Annotation maps describing the entire Gene Ontology assembled using data from GO.

Suggests

Citation

Sayols, S (2023). rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. microPublication Biology. doi: 10.17912/micropub.biology.000811.

About

Reduce + Visualize GO

Resources

Readme
GPL-3.0 license
Activity
Custom properties

Stars

0 stars

Watchers

2 watching

Forks

0 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 - imbforge/rrvgo: Reduce + Visualize GO · GitHub
Skip to content
BranchesTags
Repository files navigation
Build Status
RRVGO
Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.
Introduction to rrvgo
Gene Ontologies (GO) are often used to guide the interpretation of high-throughput
omics experiments, with lists of differentially regulated genes being summarized
into sets of genes with a common functional representation. Due to the hierachical
nature of Gene Ontologies, the resulting lists of enriched sets are usually
redundant and difficult to interpret.
rrvgo aims at simplifying the redundance of GO sets by grouping similar terms
in terms of semantic similarity. It also provides some plots to help with
interpreting the summarized terms.
This software is heavily influenced by REVIGO. It mimics
a good part of its core functionality, and even some of the outputs are similar.
Without aims to compete, rrvgo tries to offer a programatic interface using
available annotation databases and semantic similarity methods implemented in the
Bioconductor project.
Installation
To install this package, start R and enter:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("rrvgo")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rrvgo")
or access the pkgdown documentation.
Dependencies
Imports (mandatory for core functionality)
  • GOSemSim: Semantic similarity computation among GO terms.
  • AnnotationDbi: Provides user interface and database connection code for annotation data packages using SQLite data storage.
  • GO.db: Annotation maps describing the entire Gene Ontology assembled using data from GO.
Suggests
Citation
Sayols, S (2023). rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. microPublication Biology. doi: 10.17912/micropub.biology.000811.
About
Reduce + Visualize GO
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
2 watching
Forks
0 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 - imbforge/rrvgo: Reduce + Visualize GO · GitHub
Skip to content
BranchesTags
Repository files navigation
Build Status
RRVGO
Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.
Introduction to rrvgo
Gene Ontologies (GO) are often used to guide the interpretation of high-throughput
omics experiments, with lists of differentially regulated genes being summarized
into sets of genes with a common functional representation. Due to the hierachical
nature of Gene Ontologies, the resulting lists of enriched sets are usually
redundant and difficult to interpret.
rrvgo aims at simplifying the redundance of GO sets by grouping similar terms
in terms of semantic similarity. It also provides some plots to help with
interpreting the summarized terms.
This software is heavily influenced by REVIGO. It mimics
a good part of its core functionality, and even some of the outputs are similar.
Without aims to compete, rrvgo tries to offer a programatic interface using
available annotation databases and semantic similarity methods implemented in the
Bioconductor project.
Installation
To install this package, start R and enter:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("rrvgo")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rrvgo")
or access the pkgdown documentation.
Dependencies
Imports (mandatory for core functionality)
  • GOSemSim: Semantic similarity computation among GO terms.
  • AnnotationDbi: Provides user interface and database connection code for annotation data packages using SQLite data storage.
  • GO.db: Annotation maps describing the entire Gene Ontology assembled using data from GO.
Suggests
Citation
Sayols, S (2023). rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. microPublication Biology. doi: 10.17912/micropub.biology.000811.
About
Reduce + Visualize GO
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
2 watching
Forks
0 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 - imbforge/rrvgo: Reduce + Visualize GO · GitHub
Skip to content
BranchesTags
Repository files navigation
Build Status
RRVGO
Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.
Introduction to rrvgo
Gene Ontologies (GO) are often used to guide the interpretation of high-throughput
omics experiments, with lists of differentially regulated genes being summarized
into sets of genes with a common functional representation. Due to the hierachical
nature of Gene Ontologies, the resulting lists of enriched sets are usually
redundant and difficult to interpret.
rrvgo aims at simplifying the redundance of GO sets by grouping similar terms
in terms of semantic similarity. It also provides some plots to help with
interpreting the summarized terms.
This software is heavily influenced by REVIGO. It mimics
a good part of its core functionality, and even some of the outputs are similar.
Without aims to compete, rrvgo tries to offer a programatic interface using
available annotation databases and semantic similarity methods implemented in the
Bioconductor project.
Installation
To install this package, start R and enter:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("rrvgo")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rrvgo")
or access the pkgdown documentation.
Dependencies
Imports (mandatory for core functionality)
  • GOSemSim: Semantic similarity computation among GO terms.
  • AnnotationDbi: Provides user interface and database connection code for annotation data packages using SQLite data storage.
  • GO.db: Annotation maps describing the entire Gene Ontology assembled using data from GO.
Suggests
Citation
Sayols, S (2023). rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. microPublication Biology. doi: 10.17912/micropub.biology.000811.
About
Reduce + Visualize GO
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
2 watching
Forks
0 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 - imbforge/rrvgo: Reduce + Visualize GO · GitHub
Skip to content
BranchesTags
Repository files navigation
Build Status
RRVGO
Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.
Introduction to rrvgo
Gene Ontologies (GO) are often used to guide the interpretation of high-throughput
omics experiments, with lists of differentially regulated genes being summarized
into sets of genes with a common functional representation. Due to the hierachical
nature of Gene Ontologies, the resulting lists of enriched sets are usually
redundant and difficult to interpret.
rrvgo aims at simplifying the redundance of GO sets by grouping similar terms
in terms of semantic similarity. It also provides some plots to help with
interpreting the summarized terms.
This software is heavily influenced by REVIGO. It mimics
a good part of its core functionality, and even some of the outputs are similar.
Without aims to compete, rrvgo tries to offer a programatic interface using
available annotation databases and semantic similarity methods implemented in the
Bioconductor project.
Installation
To install this package, start R and enter:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("rrvgo")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rrvgo")
or access the pkgdown documentation.
Dependencies
Imports (mandatory for core functionality)
  • GOSemSim: Semantic similarity computation among GO terms.
  • AnnotationDbi: Provides user interface and database connection code for annotation data packages using SQLite data storage.
  • GO.db: Annotation maps describing the entire Gene Ontology assembled using data from GO.
Suggests
Citation
Sayols, S (2023). rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. microPublication Biology. doi: 10.17912/micropub.biology.000811.
About
Reduce + Visualize GO
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
2 watching
Forks
0 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 - imbforge/rrvgo: Reduce + Visualize GO · GitHub
Skip to content
BranchesTags
Repository files navigation
Build Status
RRVGO
Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.
Introduction to rrvgo
Gene Ontologies (GO) are often used to guide the interpretation of high-throughput
omics experiments, with lists of differentially regulated genes being summarized
into sets of genes with a common functional representation. Due to the hierachical
nature of Gene Ontologies, the resulting lists of enriched sets are usually
redundant and difficult to interpret.
rrvgo aims at simplifying the redundance of GO sets by grouping similar terms
in terms of semantic similarity. It also provides some plots to help with
interpreting the summarized terms.
This software is heavily influenced by REVIGO. It mimics
a good part of its core functionality, and even some of the outputs are similar.
Without aims to compete, rrvgo tries to offer a programatic interface using
available annotation databases and semantic similarity methods implemented in the
Bioconductor project.
Installation
To install this package, start R and enter:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("rrvgo")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rrvgo")
or access the pkgdown documentation.
Dependencies
Imports (mandatory for core functionality)
  • GOSemSim: Semantic similarity computation among GO terms.
  • AnnotationDbi: Provides user interface and database connection code for annotation data packages using SQLite data storage.
  • GO.db: Annotation maps describing the entire Gene Ontology assembled using data from GO.
Suggests
Citation
Sayols, S (2023). rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. microPublication Biology. doi: 10.17912/micropub.biology.000811.
About
Reduce + Visualize GO
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
2 watching
Forks
0 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 - imbforge/rrvgo: Reduce + Visualize GO · GitHub
Skip to content
BranchesTags
Repository files navigation
Build Status
RRVGO
Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.
Introduction to rrvgo
Gene Ontologies (GO) are often used to guide the interpretation of high-throughput
omics experiments, with lists of differentially regulated genes being summarized
into sets of genes with a common functional representation. Due to the hierachical
nature of Gene Ontologies, the resulting lists of enriched sets are usually
redundant and difficult to interpret.
rrvgo aims at simplifying the redundance of GO sets by grouping similar terms
in terms of semantic similarity. It also provides some plots to help with
interpreting the summarized terms.
This software is heavily influenced by REVIGO. It mimics
a good part of its core functionality, and even some of the outputs are similar.
Without aims to compete, rrvgo tries to offer a programatic interface using
available annotation databases and semantic similarity methods implemented in the
Bioconductor project.
Installation
To install this package, start R and enter:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("rrvgo")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rrvgo")
or access the pkgdown documentation.
Dependencies
Imports (mandatory for core functionality)
  • GOSemSim: Semantic similarity computation among GO terms.
  • AnnotationDbi: Provides user interface and database connection code for annotation data packages using SQLite data storage.
  • GO.db: Annotation maps describing the entire Gene Ontology assembled using data from GO.
Suggests
Citation
Sayols, S (2023). rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. microPublication Biology. doi: 10.17912/micropub.biology.000811.
About
Reduce + Visualize GO
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
2 watching
Forks
0 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 - imbforge/rrvgo: Reduce + Visualize GO · GitHub
Skip to content
BranchesTags
Repository files navigation
Build Status
RRVGO
Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.
Introduction to rrvgo
Gene Ontologies (GO) are often used to guide the interpretation of high-throughput
omics experiments, with lists of differentially regulated genes being summarized
into sets of genes with a common functional representation. Due to the hierachical
nature of Gene Ontologies, the resulting lists of enriched sets are usually
redundant and difficult to interpret.
rrvgo aims at simplifying the redundance of GO sets by grouping similar terms
in terms of semantic similarity. It also provides some plots to help with
interpreting the summarized terms.
This software is heavily influenced by REVIGO. It mimics
a good part of its core functionality, and even some of the outputs are similar.
Without aims to compete, rrvgo tries to offer a programatic interface using
available annotation databases and semantic similarity methods implemented in the
Bioconductor project.
Installation
To install this package, start R and enter:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("rrvgo")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rrvgo")
or access the pkgdown documentation.
Dependencies
Imports (mandatory for core functionality)
  • GOSemSim: Semantic similarity computation among GO terms.
  • AnnotationDbi: Provides user interface and database connection code for annotation data packages using SQLite data storage.
  • GO.db: Annotation maps describing the entire Gene Ontology assembled using data from GO.
Suggests
Citation
Sayols, S (2023). rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. microPublication Biology. doi: 10.17912/micropub.biology.000811.
About
Reduce + Visualize GO
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
2 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages