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Riborex

Riborex is a R package for identification of differential translation from Ribo-seq data.

Online Paper | PDF | Supplementary File

DEPENDENCIES

  • DESeq2
  • edgeR
  • fdrtool

INSTALLATION

We strongly recommend that you install Riborex via conda:

 conda install -c bioconda r-riborex

To install locally, please make sure you have DESeq2 and edgeR installed. Then start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
biocLite("edgeR")
biocLite('fdrtool')

To install Riborex, download the latest version "riborex-x.x.x.tar.gz" from releases at https://github.com/smithlabcode/riborex, start a terminal and CD into the directory where you downloaded Riborex, start R and enter

 install.packages("riborex-x.x.x.tar.gz", repos=NULL, type="source")

Alternatively, you could also install devtools package and then install riborex to get latest changes :

 install.packages('devtools')
library(devtools)
options(unzip='internal')
devtools::install_github('smithlabcode/riborex')

DOCUMENTATION

Please refer to vignettes/riborex.pdf for how to use riborex.

Contacts and bug reports

Andrew D. Smith andrewds@usc.edu

Wenzheng Li wenzhenl@usc.edu

Weili Wang weiliw@usc.edu

If you found a bug or mistake in this project, we would like to know about it. Before you send us the bug report though, please check the following:

  1. Are you using the latest version? The bug you found may already have been fixed.
  2. Check that your input is in the correct format and you have selected the correct options.
  3. Please reduce your input to the smallest possible size that still produces the bug; we will need your input data to reproduce the problem, and the smaller you can make it, the easier it will be.

Copyright and License Information

Copyright (C) 2017-2020 University of Southern California, Wenzheng Li, Weili Wang and Andrew D. Smith

Authors: Wenzheng Li, Weili Wang, Philip J. Uren, Luiz OF Penalva, Andrew D. Smith

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

About

Riborex: Fast and flexible identification of differential translation from Ribo-seq data

Topics

differential-translationriborexriboseqribosome-profiling

Resources

Readme
Activity
Custom properties

Stars

12 stars

Watchers

13 watching

Forks

2 forks
Report repository

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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DESCRIPTION
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NAMESPACE
README.md
README.md
Repository files navigation
Riborex
Riborex is a R package for identification of differential translation from Ribo-seq data.
Online Paper | PDF | Supplementary File
DEPENDENCIES
  • DESeq2
  • edgeR
  • fdrtool
INSTALLATION
We strongly recommend that you install Riborex via conda:
 conda install -c bioconda r-riborex
To install locally, please make sure you have DESeq2 and edgeR installed.
Then start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
biocLite("edgeR")
biocLite('fdrtool')
To install Riborex, download the latest version
"riborex-x.x.x.tar.gz" from releases
at https://github.com/smithlabcode/riborex, start
a terminal and CD into the directory where you downloaded Riborex,
start R and enter
 install.packages("riborex-x.x.x.tar.gz", repos=NULL, type="source")
Alternatively, you could also install devtools package and then install
riborex to get latest changes :
 install.packages('devtools')
library(devtools)
options(unzip='internal')
devtools::install_github('smithlabcode/riborex')
DOCUMENTATION
Please refer to vignettes/riborex.pdf for how to use riborex.
Contacts and bug reports
Andrew D. Smith
andrewds@usc.edu
Wenzheng Li
wenzhenl@usc.edu
Weili Wang
weiliw@usc.edu
If you found a bug or mistake in this project, we would like to know about it.
Before you send us the bug report though, please check the following:
  1. Are you using the latest version? The bug you found may already have been
fixed.
  2. Check that your input is in the correct format and you have selected the
correct options.
  3. Please reduce your input to the smallest possible size that still produces
the bug; we will need your input data to reproduce the problem, and the
smaller you can make it, the easier it will be.
Copyright and License Information
Copyright (C) 2017-2020 University of Southern California, Wenzheng Li, Weili Wang
and Andrew D. Smith
Authors: Wenzheng Li, Weili Wang, Philip J. Uren, Luiz OF Penalva, Andrew D. Smith
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program. If not, see http://www.gnu.org/licenses/.
About
Riborex: Fast and flexible identification of differential translation from Ribo-seq data
Topics
differential-translationriborexriboseqribosome-profiling
Resources
Readme
Activity
Custom properties
Stars
12 stars
Watchers
13 watching
Forks
2 forks
Report repository
Releases
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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CHANGELOG.md
DESCRIPTION
DESCRIPTION
NAMESPACE
NAMESPACE
README.md
README.md
Repository files navigation
Riborex
Riborex is a R package for identification of differential translation from Ribo-seq data.
Online Paper | PDF | Supplementary File
DEPENDENCIES
  • DESeq2
  • edgeR
  • fdrtool
INSTALLATION
We strongly recommend that you install Riborex via conda:
 conda install -c bioconda r-riborex
To install locally, please make sure you have DESeq2 and edgeR installed.
Then start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
biocLite("edgeR")
biocLite('fdrtool')
To install Riborex, download the latest version
"riborex-x.x.x.tar.gz" from releases
at https://github.com/smithlabcode/riborex, start
a terminal and CD into the directory where you downloaded Riborex,
start R and enter
 install.packages("riborex-x.x.x.tar.gz", repos=NULL, type="source")
Alternatively, you could also install devtools package and then install
riborex to get latest changes :
 install.packages('devtools')
library(devtools)
options(unzip='internal')
devtools::install_github('smithlabcode/riborex')
DOCUMENTATION
Please refer to vignettes/riborex.pdf for how to use riborex.
Contacts and bug reports
Andrew D. Smith
andrewds@usc.edu
Wenzheng Li
wenzhenl@usc.edu
Weili Wang
weiliw@usc.edu
If you found a bug or mistake in this project, we would like to know about it.
Before you send us the bug report though, please check the following:
  1. Are you using the latest version? The bug you found may already have been
fixed.
  2. Check that your input is in the correct format and you have selected the
correct options.
  3. Please reduce your input to the smallest possible size that still produces
the bug; we will need your input data to reproduce the problem, and the
smaller you can make it, the easier it will be.
Copyright and License Information
Copyright (C) 2017-2020 University of Southern California, Wenzheng Li, Weili Wang
and Andrew D. Smith
Authors: Wenzheng Li, Weili Wang, Philip J. Uren, Luiz OF Penalva, Andrew D. Smith
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program. If not, see http://www.gnu.org/licenses/.
About
Riborex: Fast and flexible identification of differential translation from Ribo-seq data
Topics
differential-translationriborexriboseqribosome-profiling
Resources
Readme
Activity
Custom properties
Stars
12 stars
Watchers
13 watching
Forks
2 forks
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('^' + ".*" + '

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.gitignore
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CHANGELOG.md
DESCRIPTION
DESCRIPTION
NAMESPACE
NAMESPACE
README.md
README.md
Repository files navigation
Riborex
Riborex is a R package for identification of differential translation from Ribo-seq data.
Online Paper | PDF | Supplementary File
DEPENDENCIES
  • DESeq2
  • edgeR
  • fdrtool
INSTALLATION
We strongly recommend that you install Riborex via conda:
 conda install -c bioconda r-riborex
To install locally, please make sure you have DESeq2 and edgeR installed.
Then start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
biocLite("edgeR")
biocLite('fdrtool')
To install Riborex, download the latest version
"riborex-x.x.x.tar.gz" from releases
at https://github.com/smithlabcode/riborex, start
a terminal and CD into the directory where you downloaded Riborex,
start R and enter
 install.packages("riborex-x.x.x.tar.gz", repos=NULL, type="source")
Alternatively, you could also install devtools package and then install
riborex to get latest changes :
 install.packages('devtools')
library(devtools)
options(unzip='internal')
devtools::install_github('smithlabcode/riborex')
DOCUMENTATION
Please refer to vignettes/riborex.pdf for how to use riborex.
Contacts and bug reports
Andrew D. Smith
andrewds@usc.edu
Wenzheng Li
wenzhenl@usc.edu
Weili Wang
weiliw@usc.edu
If you found a bug or mistake in this project, we would like to know about it.
Before you send us the bug report though, please check the following:
  1. Are you using the latest version? The bug you found may already have been
fixed.
  2. Check that your input is in the correct format and you have selected the
correct options.
  3. Please reduce your input to the smallest possible size that still produces
the bug; we will need your input data to reproduce the problem, and the
smaller you can make it, the easier it will be.
Copyright and License Information
Copyright (C) 2017-2020 University of Southern California, Wenzheng Li, Weili Wang
and Andrew D. Smith
Authors: Wenzheng Li, Weili Wang, Philip J. Uren, Luiz OF Penalva, Andrew D. Smith
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program. If not, see http://www.gnu.org/licenses/.
About
Riborex: Fast and flexible identification of differential translation from Ribo-seq data
Topics
differential-translationriborexriboseqribosome-profiling
Resources
Readme
Activity
Custom properties
Stars
12 stars
Watchers
13 watching
Forks
2 forks
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" + '

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.gitignore
CHANGELOG.md
CHANGELOG.md
DESCRIPTION
DESCRIPTION
NAMESPACE
NAMESPACE
README.md
README.md
Repository files navigation
Riborex
Riborex is a R package for identification of differential translation from Ribo-seq data.
Online Paper | PDF | Supplementary File
DEPENDENCIES
  • DESeq2
  • edgeR
  • fdrtool
INSTALLATION
We strongly recommend that you install Riborex via conda:
 conda install -c bioconda r-riborex
To install locally, please make sure you have DESeq2 and edgeR installed.
Then start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
biocLite("edgeR")
biocLite('fdrtool')
To install Riborex, download the latest version
"riborex-x.x.x.tar.gz" from releases
at https://github.com/smithlabcode/riborex, start
a terminal and CD into the directory where you downloaded Riborex,
start R and enter
 install.packages("riborex-x.x.x.tar.gz", repos=NULL, type="source")
Alternatively, you could also install devtools package and then install
riborex to get latest changes :
 install.packages('devtools')
library(devtools)
options(unzip='internal')
devtools::install_github('smithlabcode/riborex')
DOCUMENTATION
Please refer to vignettes/riborex.pdf for how to use riborex.
Contacts and bug reports
Andrew D. Smith
andrewds@usc.edu
Wenzheng Li
wenzhenl@usc.edu
Weili Wang
weiliw@usc.edu
If you found a bug or mistake in this project, we would like to know about it.
Before you send us the bug report though, please check the following:
  1. Are you using the latest version? The bug you found may already have been
fixed.
  2. Check that your input is in the correct format and you have selected the
correct options.
  3. Please reduce your input to the smallest possible size that still produces
the bug; we will need your input data to reproduce the problem, and the
smaller you can make it, the easier it will be.
Copyright and License Information
Copyright (C) 2017-2020 University of Southern California, Wenzheng Li, Weili Wang
and Andrew D. Smith
Authors: Wenzheng Li, Weili Wang, Philip J. Uren, Luiz OF Penalva, Andrew D. Smith
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program. If not, see http://www.gnu.org/licenses/.
About
Riborex: Fast and flexible identification of differential translation from Ribo-seq data
Topics
differential-translationriborexriboseqribosome-profiling
Resources
Readme
Activity
Custom properties
Stars
12 stars
Watchers
13 watching
Forks
2 forks
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('^' + ".*" + '

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.gitignore
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CHANGELOG.md
DESCRIPTION
DESCRIPTION
NAMESPACE
NAMESPACE
README.md
README.md
Repository files navigation
Riborex
Riborex is a R package for identification of differential translation from Ribo-seq data.
Online Paper | PDF | Supplementary File
DEPENDENCIES
  • DESeq2
  • edgeR
  • fdrtool
INSTALLATION
We strongly recommend that you install Riborex via conda:
 conda install -c bioconda r-riborex
To install locally, please make sure you have DESeq2 and edgeR installed.
Then start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
biocLite("edgeR")
biocLite('fdrtool')
To install Riborex, download the latest version
"riborex-x.x.x.tar.gz" from releases
at https://github.com/smithlabcode/riborex, start
a terminal and CD into the directory where you downloaded Riborex,
start R and enter
 install.packages("riborex-x.x.x.tar.gz", repos=NULL, type="source")
Alternatively, you could also install devtools package and then install
riborex to get latest changes :
 install.packages('devtools')
library(devtools)
options(unzip='internal')
devtools::install_github('smithlabcode/riborex')
DOCUMENTATION
Please refer to vignettes/riborex.pdf for how to use riborex.
Contacts and bug reports
Andrew D. Smith
andrewds@usc.edu
Wenzheng Li
wenzhenl@usc.edu
Weili Wang
weiliw@usc.edu
If you found a bug or mistake in this project, we would like to know about it.
Before you send us the bug report though, please check the following:
  1. Are you using the latest version? The bug you found may already have been
fixed.
  2. Check that your input is in the correct format and you have selected the
correct options.
  3. Please reduce your input to the smallest possible size that still produces
the bug; we will need your input data to reproduce the problem, and the
smaller you can make it, the easier it will be.
Copyright and License Information
Copyright (C) 2017-2020 University of Southern California, Wenzheng Li, Weili Wang
and Andrew D. Smith
Authors: Wenzheng Li, Weili Wang, Philip J. Uren, Luiz OF Penalva, Andrew D. Smith
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program. If not, see http://www.gnu.org/licenses/.
About
Riborex: Fast and flexible identification of differential translation from Ribo-seq data
Topics
differential-translationriborexriboseqribosome-profiling
Resources
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12 stars
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13 watching
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2 forks
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, '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('^' + ".*" + '

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DESCRIPTION
DESCRIPTION
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README.md
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Repository files navigation
Riborex
Riborex is a R package for identification of differential translation from Ribo-seq data.
Online Paper | PDF | Supplementary File
DEPENDENCIES
  • DESeq2
  • edgeR
  • fdrtool
INSTALLATION
We strongly recommend that you install Riborex via conda:
 conda install -c bioconda r-riborex
To install locally, please make sure you have DESeq2 and edgeR installed.
Then start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
biocLite("edgeR")
biocLite('fdrtool')
To install Riborex, download the latest version
"riborex-x.x.x.tar.gz" from releases
at https://github.com/smithlabcode/riborex, start
a terminal and CD into the directory where you downloaded Riborex,
start R and enter
 install.packages("riborex-x.x.x.tar.gz", repos=NULL, type="source")
Alternatively, you could also install devtools package and then install
riborex to get latest changes :
 install.packages('devtools')
library(devtools)
options(unzip='internal')
devtools::install_github('smithlabcode/riborex')
DOCUMENTATION
Please refer to vignettes/riborex.pdf for how to use riborex.
Contacts and bug reports
Andrew D. Smith
andrewds@usc.edu
Wenzheng Li
wenzhenl@usc.edu
Weili Wang
weiliw@usc.edu
If you found a bug or mistake in this project, we would like to know about it.
Before you send us the bug report though, please check the following:
  1. Are you using the latest version? The bug you found may already have been
fixed.
  2. Check that your input is in the correct format and you have selected the
correct options.
  3. Please reduce your input to the smallest possible size that still produces
the bug; we will need your input data to reproduce the problem, and the
smaller you can make it, the easier it will be.
Copyright and License Information
Copyright (C) 2017-2020 University of Southern California, Wenzheng Li, Weili Wang
and Andrew D. Smith
Authors: Wenzheng Li, Weili Wang, Philip J. Uren, Luiz OF Penalva, Andrew D. Smith
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program. If not, see http://www.gnu.org/licenses/.
About
Riborex: Fast and flexible identification of differential translation from Ribo-seq data
Topics
differential-translationriborexriboseqribosome-profiling
Resources
Readme
Activity
Custom properties
Stars
12 stars
Watchers
13 watching
Forks
2 forks
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
Latest commit
History
121 Commits
Folders and files
NameName
Last commit message
Last commit date
R
R
data
data
inst
inst
man
man
vignettes
vignettes
.gitignore
.gitignore
CHANGELOG.md
CHANGELOG.md
DESCRIPTION
DESCRIPTION
NAMESPACE
NAMESPACE
README.md
README.md
Repository files navigation
Riborex
Riborex is a R package for identification of differential translation from Ribo-seq data.
Online Paper | PDF | Supplementary File
DEPENDENCIES
  • DESeq2
  • edgeR
  • fdrtool
INSTALLATION
We strongly recommend that you install Riborex via conda:
 conda install -c bioconda r-riborex
To install locally, please make sure you have DESeq2 and edgeR installed.
Then start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
biocLite("edgeR")
biocLite('fdrtool')
To install Riborex, download the latest version
"riborex-x.x.x.tar.gz" from releases
at https://github.com/smithlabcode/riborex, start
a terminal and CD into the directory where you downloaded Riborex,
start R and enter
 install.packages("riborex-x.x.x.tar.gz", repos=NULL, type="source")
Alternatively, you could also install devtools package and then install
riborex to get latest changes :
 install.packages('devtools')
library(devtools)
options(unzip='internal')
devtools::install_github('smithlabcode/riborex')
DOCUMENTATION
Please refer to vignettes/riborex.pdf for how to use riborex.
Contacts and bug reports
Andrew D. Smith
andrewds@usc.edu
Wenzheng Li
wenzhenl@usc.edu
Weili Wang
weiliw@usc.edu
If you found a bug or mistake in this project, we would like to know about it.
Before you send us the bug report though, please check the following:
  1. Are you using the latest version? The bug you found may already have been
fixed.
  2. Check that your input is in the correct format and you have selected the
correct options.
  3. Please reduce your input to the smallest possible size that still produces
the bug; we will need your input data to reproduce the problem, and the
smaller you can make it, the easier it will be.
Copyright and License Information
Copyright (C) 2017-2020 University of Southern California, Wenzheng Li, Weili Wang
and Andrew D. Smith
Authors: Wenzheng Li, Weili Wang, Philip J. Uren, Luiz OF Penalva, Andrew D. Smith
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program. If not, see http://www.gnu.org/licenses/.
About
Riborex: Fast and flexible identification of differential translation from Ribo-seq data
Topics
differential-translationriborexriboseqribosome-profiling
Resources
Readme
Activity
Custom properties
Stars
12 stars
Watchers
13 watching
Forks
2 forks
Report repository
Releases
Packages
Contributors
Languages