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scseq

This repository contains scripts and tools for single cell RNAseq, as initially developed by Dominic Grün and Alexander van Oudenaarden at the Hubrecht Institute, Utrecht, The Netherlands.

This code has moved to https://bitbucket.org/princessmaximacenter/scseq/ .Contact me if you want access.

It contains (often heavily modified) code from other people, specifically from Dominic Grün (now at MPI Freiburg), Lennart Kester and Abel Vertesy. For related code, see Abel Vertesy's repository, in particular the Python/MapAndGo and Python/Concatenator subdirectories

Contents

General stuff

  • env.sh.example - sets PATH en PERLLIB so they don't have to be hard-coded
  • tools.pm - functions used by the perl scripts

barcodes and external controls

  • holstegelab_EC.fa - kept for historic reasons
  • ERCC92.fa - superset of holstegelab_EC.fa, well-known set of external spike-in controls
  • cel-seq96_barcodes.csv - initial set of barcodes
  • celseq2_bc384.csv - barcodes used for celseq2, 384-well protocols

preparing the reference transcriptome

  • mask_polyA.pl - masks any /A{10,}/ in reference transcriptome
  • ucsc2gtf.pl - converts UCSC RefSeq.txt table to a gtf file
  • polyXY.pl - finds stretches of e.g. AAAAAAAAGGGGGGGG etc.
  • merge_isoforms_gtf.pl - creates 'supertranscripts', i.e. (virtual) transcripts consisting of all possible exons

mapping and postprocessing

  • do_mappings_strand_cs2v2.pl - driver script for preprocssing, mapping and bookkeeping. See also Abel Vertesy's Python/MapAndGo/MapAndGo.py in https://github.com/vertesy/TheCorvinas
  • add_bc_to_R2.pl - preprocesses the reads prior to mapping.
  • process_sam_cel384v2.pl - bookkeeping and statistics per cell. Needs code from https://github.com/plijnzaad/demultiplex for recovering mismatched cell barcodes

About

Scripts and tools for single cell RNAseq. This code has moved to https://bitbucket.org/princessmaximacenter/scseq/

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try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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scseq
This repository contains scripts and tools for single cell RNAseq, as
initially developed by Dominic Grün and Alexander van Oudenaarden at the
Hubrecht Institute, Utrecht, The Netherlands.
This code has moved to https://bitbucket.org/princessmaximacenter/scseq/ .Contact me if you want access.
It contains (often heavily modified) code from other people,
specifically from Dominic Grün (now at MPI Freiburg), Lennart Kester and
Abel Vertesy. For related code,
see Abel Vertesy's repository,
in particular the Python/MapAndGo and Python/Concatenator subdirectories
Contents
General stuff
  • env.sh.example - sets PATH en PERLLIB so they don't have to be hard-coded
  • tools.pm - functions used by the perl scripts
barcodes and external controls
  • holstegelab_EC.fa - kept for historic reasons
  • ERCC92.fa - superset of holstegelab_EC.fa, well-known set of external spike-in controls
  • cel-seq96_barcodes.csv - initial set of barcodes
  • celseq2_bc384.csv - barcodes used for celseq2, 384-well protocols
preparing the reference transcriptome
  • mask_polyA.pl - masks any /A{10,}/ in reference transcriptome
  • ucsc2gtf.pl - converts UCSC RefSeq.txt table to a gtf file
  • polyXY.pl - finds stretches of e.g. AAAAAAAAGGGGGGGG etc.
  • merge_isoforms_gtf.pl - creates 'supertranscripts', i.e. (virtual) transcripts consisting of all possible exons
mapping and postprocessing
  • do_mappings_strand_cs2v2.pl - driver script for preprocssing, mapping and bookkeeping. See also Abel Vertesy's Python/MapAndGo/MapAndGo.py in https://github.com/vertesy/TheCorvinas
  • add_bc_to_R2.pl - preprocesses the reads prior to mapping.
  • process_sam_cel384v2.pl - bookkeeping and statistics per cell. Needs code from https://github.com/plijnzaad/demultiplex for recovering mismatched cell barcodes
About
Scripts and tools for single cell RNAseq. This code has moved to https://bitbucket.org/princessmaximacenter/scseq/
Resources
Readme
Activity
Stars
1 star
Watchers
1 watching
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, 'i');
if (__m === '*' || __re.test(location.href)) {
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})();
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var __m = "*";
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scseq
This repository contains scripts and tools for single cell RNAseq, as
initially developed by Dominic Grün and Alexander van Oudenaarden at the
Hubrecht Institute, Utrecht, The Netherlands.
This code has moved to https://bitbucket.org/princessmaximacenter/scseq/ .Contact me if you want access.
It contains (often heavily modified) code from other people,
specifically from Dominic Grün (now at MPI Freiburg), Lennart Kester and
Abel Vertesy. For related code,
see Abel Vertesy's repository,
in particular the Python/MapAndGo and Python/Concatenator subdirectories
Contents
General stuff
  • env.sh.example - sets PATH en PERLLIB so they don't have to be hard-coded
  • tools.pm - functions used by the perl scripts
barcodes and external controls
  • holstegelab_EC.fa - kept for historic reasons
  • ERCC92.fa - superset of holstegelab_EC.fa, well-known set of external spike-in controls
  • cel-seq96_barcodes.csv - initial set of barcodes
  • celseq2_bc384.csv - barcodes used for celseq2, 384-well protocols
preparing the reference transcriptome
  • mask_polyA.pl - masks any /A{10,}/ in reference transcriptome
  • ucsc2gtf.pl - converts UCSC RefSeq.txt table to a gtf file
  • polyXY.pl - finds stretches of e.g. AAAAAAAAGGGGGGGG etc.
  • merge_isoforms_gtf.pl - creates 'supertranscripts', i.e. (virtual) transcripts consisting of all possible exons
mapping and postprocessing
  • do_mappings_strand_cs2v2.pl - driver script for preprocssing, mapping and bookkeeping. See also Abel Vertesy's Python/MapAndGo/MapAndGo.py in https://github.com/vertesy/TheCorvinas
  • add_bc_to_R2.pl - preprocesses the reads prior to mapping.
  • process_sam_cel384v2.pl - bookkeeping and statistics per cell. Needs code from https://github.com/plijnzaad/demultiplex for recovering mismatched cell barcodes
About
Scripts and tools for single cell RNAseq. This code has moved to https://bitbucket.org/princessmaximacenter/scseq/
Resources
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, 'i');
if (__m === '*' || __re.test(location.href)) {
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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scseq
This repository contains scripts and tools for single cell RNAseq, as
initially developed by Dominic Grün and Alexander van Oudenaarden at the
Hubrecht Institute, Utrecht, The Netherlands.
This code has moved to https://bitbucket.org/princessmaximacenter/scseq/ .Contact me if you want access.
It contains (often heavily modified) code from other people,
specifically from Dominic Grün (now at MPI Freiburg), Lennart Kester and
Abel Vertesy. For related code,
see Abel Vertesy's repository,
in particular the Python/MapAndGo and Python/Concatenator subdirectories
Contents
General stuff
  • env.sh.example - sets PATH en PERLLIB so they don't have to be hard-coded
  • tools.pm - functions used by the perl scripts
barcodes and external controls
  • holstegelab_EC.fa - kept for historic reasons
  • ERCC92.fa - superset of holstegelab_EC.fa, well-known set of external spike-in controls
  • cel-seq96_barcodes.csv - initial set of barcodes
  • celseq2_bc384.csv - barcodes used for celseq2, 384-well protocols
preparing the reference transcriptome
  • mask_polyA.pl - masks any /A{10,}/ in reference transcriptome
  • ucsc2gtf.pl - converts UCSC RefSeq.txt table to a gtf file
  • polyXY.pl - finds stretches of e.g. AAAAAAAAGGGGGGGG etc.
  • merge_isoforms_gtf.pl - creates 'supertranscripts', i.e. (virtual) transcripts consisting of all possible exons
mapping and postprocessing
  • do_mappings_strand_cs2v2.pl - driver script for preprocssing, mapping and bookkeeping. See also Abel Vertesy's Python/MapAndGo/MapAndGo.py in https://github.com/vertesy/TheCorvinas
  • add_bc_to_R2.pl - preprocesses the reads prior to mapping.
  • process_sam_cel384v2.pl - bookkeeping and statistics per cell. Needs code from https://github.com/plijnzaad/demultiplex for recovering mismatched cell barcodes
About
Scripts and tools for single cell RNAseq. This code has moved to https://bitbucket.org/princessmaximacenter/scseq/
Resources
Readme
Activity
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, '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");
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} 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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scseq
This repository contains scripts and tools for single cell RNAseq, as
initially developed by Dominic Grün and Alexander van Oudenaarden at the
Hubrecht Institute, Utrecht, The Netherlands.
This code has moved to https://bitbucket.org/princessmaximacenter/scseq/ .Contact me if you want access.
It contains (often heavily modified) code from other people,
specifically from Dominic Grün (now at MPI Freiburg), Lennart Kester and
Abel Vertesy. For related code,
see Abel Vertesy's repository,
in particular the Python/MapAndGo and Python/Concatenator subdirectories
Contents
General stuff
  • env.sh.example - sets PATH en PERLLIB so they don't have to be hard-coded
  • tools.pm - functions used by the perl scripts
barcodes and external controls
  • holstegelab_EC.fa - kept for historic reasons
  • ERCC92.fa - superset of holstegelab_EC.fa, well-known set of external spike-in controls
  • cel-seq96_barcodes.csv - initial set of barcodes
  • celseq2_bc384.csv - barcodes used for celseq2, 384-well protocols
preparing the reference transcriptome
  • mask_polyA.pl - masks any /A{10,}/ in reference transcriptome
  • ucsc2gtf.pl - converts UCSC RefSeq.txt table to a gtf file
  • polyXY.pl - finds stretches of e.g. AAAAAAAAGGGGGGGG etc.
  • merge_isoforms_gtf.pl - creates 'supertranscripts', i.e. (virtual) transcripts consisting of all possible exons
mapping and postprocessing
  • do_mappings_strand_cs2v2.pl - driver script for preprocssing, mapping and bookkeeping. See also Abel Vertesy's Python/MapAndGo/MapAndGo.py in https://github.com/vertesy/TheCorvinas
  • add_bc_to_R2.pl - preprocesses the reads prior to mapping.
  • process_sam_cel384v2.pl - bookkeeping and statistics per cell. Needs code from https://github.com/plijnzaad/demultiplex for recovering mismatched cell barcodes
About
Scripts and tools for single cell RNAseq. This code has moved to https://bitbucket.org/princessmaximacenter/scseq/
Resources
Readme
Activity
Stars
1 star
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
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, '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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scseq
This repository contains scripts and tools for single cell RNAseq, as
initially developed by Dominic Grün and Alexander van Oudenaarden at the
Hubrecht Institute, Utrecht, The Netherlands.
This code has moved to https://bitbucket.org/princessmaximacenter/scseq/ .Contact me if you want access.
It contains (often heavily modified) code from other people,
specifically from Dominic Grün (now at MPI Freiburg), Lennart Kester and
Abel Vertesy. For related code,
see Abel Vertesy's repository,
in particular the Python/MapAndGo and Python/Concatenator subdirectories
Contents
General stuff
  • env.sh.example - sets PATH en PERLLIB so they don't have to be hard-coded
  • tools.pm - functions used by the perl scripts
barcodes and external controls
  • holstegelab_EC.fa - kept for historic reasons
  • ERCC92.fa - superset of holstegelab_EC.fa, well-known set of external spike-in controls
  • cel-seq96_barcodes.csv - initial set of barcodes
  • celseq2_bc384.csv - barcodes used for celseq2, 384-well protocols
preparing the reference transcriptome
  • mask_polyA.pl - masks any /A{10,}/ in reference transcriptome
  • ucsc2gtf.pl - converts UCSC RefSeq.txt table to a gtf file
  • polyXY.pl - finds stretches of e.g. AAAAAAAAGGGGGGGG etc.
  • merge_isoforms_gtf.pl - creates 'supertranscripts', i.e. (virtual) transcripts consisting of all possible exons
mapping and postprocessing
  • do_mappings_strand_cs2v2.pl - driver script for preprocssing, mapping and bookkeeping. See also Abel Vertesy's Python/MapAndGo/MapAndGo.py in https://github.com/vertesy/TheCorvinas
  • add_bc_to_R2.pl - preprocesses the reads prior to mapping.
  • process_sam_cel384v2.pl - bookkeeping and statistics per cell. Needs code from https://github.com/plijnzaad/demultiplex for recovering mismatched cell barcodes
About
Scripts and tools for single cell RNAseq. This code has moved to https://bitbucket.org/princessmaximacenter/scseq/
Resources
Readme
Activity
Stars
1 star
Watchers
1 watching
Forks
0 forks
Report repository
Releases
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Contributors
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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");
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} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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scseq
This repository contains scripts and tools for single cell RNAseq, as
initially developed by Dominic Grün and Alexander van Oudenaarden at the
Hubrecht Institute, Utrecht, The Netherlands.
This code has moved to https://bitbucket.org/princessmaximacenter/scseq/ .Contact me if you want access.
It contains (often heavily modified) code from other people,
specifically from Dominic Grün (now at MPI Freiburg), Lennart Kester and
Abel Vertesy. For related code,
see Abel Vertesy's repository,
in particular the Python/MapAndGo and Python/Concatenator subdirectories
Contents
General stuff
  • env.sh.example - sets PATH en PERLLIB so they don't have to be hard-coded
  • tools.pm - functions used by the perl scripts
barcodes and external controls
  • holstegelab_EC.fa - kept for historic reasons
  • ERCC92.fa - superset of holstegelab_EC.fa, well-known set of external spike-in controls
  • cel-seq96_barcodes.csv - initial set of barcodes
  • celseq2_bc384.csv - barcodes used for celseq2, 384-well protocols
preparing the reference transcriptome
  • mask_polyA.pl - masks any /A{10,}/ in reference transcriptome
  • ucsc2gtf.pl - converts UCSC RefSeq.txt table to a gtf file
  • polyXY.pl - finds stretches of e.g. AAAAAAAAGGGGGGGG etc.
  • merge_isoforms_gtf.pl - creates 'supertranscripts', i.e. (virtual) transcripts consisting of all possible exons
mapping and postprocessing
  • do_mappings_strand_cs2v2.pl - driver script for preprocssing, mapping and bookkeeping. See also Abel Vertesy's Python/MapAndGo/MapAndGo.py in https://github.com/vertesy/TheCorvinas
  • add_bc_to_R2.pl - preprocesses the reads prior to mapping.
  • process_sam_cel384v2.pl - bookkeeping and statistics per cell. Needs code from https://github.com/plijnzaad/demultiplex for recovering mismatched cell barcodes
About
Scripts and tools for single cell RNAseq. This code has moved to https://bitbucket.org/princessmaximacenter/scseq/
Resources
Readme
Activity
Stars
1 star
Watchers
1 watching
Forks
0 forks
Report repository
Releases
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, '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");
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} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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scseq
This repository contains scripts and tools for single cell RNAseq, as
initially developed by Dominic Grün and Alexander van Oudenaarden at the
Hubrecht Institute, Utrecht, The Netherlands.
This code has moved to https://bitbucket.org/princessmaximacenter/scseq/ .Contact me if you want access.
It contains (often heavily modified) code from other people,
specifically from Dominic Grün (now at MPI Freiburg), Lennart Kester and
Abel Vertesy. For related code,
see Abel Vertesy's repository,
in particular the Python/MapAndGo and Python/Concatenator subdirectories
Contents
General stuff
  • env.sh.example - sets PATH en PERLLIB so they don't have to be hard-coded
  • tools.pm - functions used by the perl scripts
barcodes and external controls
  • holstegelab_EC.fa - kept for historic reasons
  • ERCC92.fa - superset of holstegelab_EC.fa, well-known set of external spike-in controls
  • cel-seq96_barcodes.csv - initial set of barcodes
  • celseq2_bc384.csv - barcodes used for celseq2, 384-well protocols
preparing the reference transcriptome
  • mask_polyA.pl - masks any /A{10,}/ in reference transcriptome
  • ucsc2gtf.pl - converts UCSC RefSeq.txt table to a gtf file
  • polyXY.pl - finds stretches of e.g. AAAAAAAAGGGGGGGG etc.
  • merge_isoforms_gtf.pl - creates 'supertranscripts', i.e. (virtual) transcripts consisting of all possible exons
mapping and postprocessing
  • do_mappings_strand_cs2v2.pl - driver script for preprocssing, mapping and bookkeeping. See also Abel Vertesy's Python/MapAndGo/MapAndGo.py in https://github.com/vertesy/TheCorvinas
  • add_bc_to_R2.pl - preprocesses the reads prior to mapping.
  • process_sam_cel384v2.pl - bookkeeping and statistics per cell. Needs code from https://github.com/plijnzaad/demultiplex for recovering mismatched cell barcodes
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Scripts and tools for single cell RNAseq. This code has moved to https://bitbucket.org/princessmaximacenter/scseq/
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