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seqcluster

Ask questions in the repo's Gitter: Join the chat at:

small RNA analysis from NGS data

https://travis-ci.org/lpantano/seqcluster.png?branch=masterhttps://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-squareProject Status: Active - The project has reached a stable, usable state and is being actively developed.https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtv632-lightgrey.svg?style=flat-square

Cite

Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis. Pantano L, Friedländer MR, Escaramís G, Lizano E, Pallarès-Albanell J, Ferrer I, Estivill X, Martí E. Bioinformatics. 2015 Nov 2. pii: btv632. [Epub ahead of print] PMID: 26530722

A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome. Pantano L1, Estivill X, Martí E. Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5. PMID: 21976421

Quick start links

See installation at http://seqcluster.readthedocs.org/installation.html

Moreover bcbio-nextgen provides a python framework to run a whole pipeline for small RNA (miRNA + tRNA + piRNA + others).

An example of how to run with bcbio is here: http://seqcluster.readthedocs.org/example_pipeline.html#mirqc-data

In case you want to use seqcluster alone, a complete tutorial is here: http://seqcluster.readthedocs.org/getting_started.html#clustering-of-small-rna-sequences

Report

Seqcluster creates html report that looks like this. That is a table of all cluster detected, and you can go into each of them and get a complete description with profile expression figures, annotation details and sequences counts for each sample. An interactive report is as well available to explore the expression profile, position on the genome and secondary structure. Learn more http://seqcluster.readthedocs.org/more_outputs.html#report.

Contributors

  • Lorena Pantano (Bioinformatic Core, Harvard Chan School, Boston, USA)
  • Judith Flo Gaya (School of Engineer and Aplied Science- Harvard University, Boston, USA)
  • Eulalia Marti Puig (Genomics and Disease, Center of Genomic Regulation, Barcelona, Spain)
  • Francisco Pantano Rubino: Architect
  • Steffen Möller (University of Rostock)
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small RNA analysis from NGS data

seqcluster.readthedocs.io

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seqcluster
Ask questions in the repo's Gitter: Join the chat at:
small RNA analysis from NGS data
https://travis-ci.org/lpantano/seqcluster.png?branch=masterhttps://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-squareProject Status: Active - The project has reached a stable, usable state and is being actively developed.https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtv632-lightgrey.svg?style=flat-square
Cite
Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis. Pantano L, Friedländer MR, Escaramís G, Lizano E, Pallarès-Albanell J, Ferrer I, Estivill X, Martí E.
Bioinformatics. 2015 Nov 2. pii: btv632. [Epub ahead of print]
PMID: 26530722
A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.
Pantano L1, Estivill X, Martí E. Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5.
PMID: 21976421
Quick start links
See installation at http://seqcluster.readthedocs.org/installation.html
Moreover bcbio-nextgen provides
a python framework to run a whole pipeline for small RNA (miRNA + tRNA + piRNA + others).
An example of how to run with bcbio is here: http://seqcluster.readthedocs.org/example_pipeline.html#mirqc-data
In case you want to use seqcluster alone, a complete tutorial is here: http://seqcluster.readthedocs.org/getting_started.html#clustering-of-small-rna-sequences
Report
Seqcluster creates html report that looks like this. That is a table of all cluster detected, and you
can go into each of them and get a complete description with profile expression figures, annotation details and
sequences counts for each sample. An interactive report is as well available to explore the expression profile,
position on the genome and secondary structure. Learn more http://seqcluster.readthedocs.org/more_outputs.html#report.
Contributors
  • Lorena Pantano (Bioinformatic Core, Harvard Chan School, Boston, USA)
  • Judith Flo Gaya (School of Engineer and Aplied Science- Harvard University, Boston, USA)
  • Eulalia Marti Puig (Genomics and Disease, Center of Genomic Regulation, Barcelona, Spain)
  • Francisco Pantano Rubino: Architect
  • Steffen Möller (University of Rostock)
Bitdeli badge
About
small RNA analysis from NGS data
seqcluster.readthedocs.io
Topics
mirnareportsequencingsmallrnatrna
Resources
Readme
MIT license
Activity
Stars
39 stars
Watchers
1 watching
Forks
19 forks
Report repository
Releases
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Used by
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, 'i');
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seqcluster
Ask questions in the repo's Gitter: Join the chat at:
small RNA analysis from NGS data
https://travis-ci.org/lpantano/seqcluster.png?branch=masterhttps://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-squareProject Status: Active - The project has reached a stable, usable state and is being actively developed.https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtv632-lightgrey.svg?style=flat-square
Cite
Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis. Pantano L, Friedländer MR, Escaramís G, Lizano E, Pallarès-Albanell J, Ferrer I, Estivill X, Martí E.
Bioinformatics. 2015 Nov 2. pii: btv632. [Epub ahead of print]
PMID: 26530722
A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.
Pantano L1, Estivill X, Martí E. Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5.
PMID: 21976421
Quick start links
See installation at http://seqcluster.readthedocs.org/installation.html
Moreover bcbio-nextgen provides
a python framework to run a whole pipeline for small RNA (miRNA + tRNA + piRNA + others).
An example of how to run with bcbio is here: http://seqcluster.readthedocs.org/example_pipeline.html#mirqc-data
In case you want to use seqcluster alone, a complete tutorial is here: http://seqcluster.readthedocs.org/getting_started.html#clustering-of-small-rna-sequences
Report
Seqcluster creates html report that looks like this. That is a table of all cluster detected, and you
can go into each of them and get a complete description with profile expression figures, annotation details and
sequences counts for each sample. An interactive report is as well available to explore the expression profile,
position on the genome and secondary structure. Learn more http://seqcluster.readthedocs.org/more_outputs.html#report.
Contributors
  • Lorena Pantano (Bioinformatic Core, Harvard Chan School, Boston, USA)
  • Judith Flo Gaya (School of Engineer and Aplied Science- Harvard University, Boston, USA)
  • Eulalia Marti Puig (Genomics and Disease, Center of Genomic Regulation, Barcelona, Spain)
  • Francisco Pantano Rubino: Architect
  • Steffen Möller (University of Rostock)
Bitdeli badge
About
small RNA analysis from NGS data
seqcluster.readthedocs.io
Topics
mirnareportsequencingsmallrnatrna
Resources
Readme
MIT license
Activity
Stars
39 stars
Watchers
1 watching
Forks
19 forks
Report repository
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Used by
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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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seqcluster
Ask questions in the repo's Gitter: Join the chat at:
small RNA analysis from NGS data
https://travis-ci.org/lpantano/seqcluster.png?branch=masterhttps://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-squareProject Status: Active - The project has reached a stable, usable state and is being actively developed.https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtv632-lightgrey.svg?style=flat-square
Cite
Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis. Pantano L, Friedländer MR, Escaramís G, Lizano E, Pallarès-Albanell J, Ferrer I, Estivill X, Martí E.
Bioinformatics. 2015 Nov 2. pii: btv632. [Epub ahead of print]
PMID: 26530722
A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.
Pantano L1, Estivill X, Martí E. Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5.
PMID: 21976421
Quick start links
See installation at http://seqcluster.readthedocs.org/installation.html
Moreover bcbio-nextgen provides
a python framework to run a whole pipeline for small RNA (miRNA + tRNA + piRNA + others).
An example of how to run with bcbio is here: http://seqcluster.readthedocs.org/example_pipeline.html#mirqc-data
In case you want to use seqcluster alone, a complete tutorial is here: http://seqcluster.readthedocs.org/getting_started.html#clustering-of-small-rna-sequences
Report
Seqcluster creates html report that looks like this. That is a table of all cluster detected, and you
can go into each of them and get a complete description with profile expression figures, annotation details and
sequences counts for each sample. An interactive report is as well available to explore the expression profile,
position on the genome and secondary structure. Learn more http://seqcluster.readthedocs.org/more_outputs.html#report.
Contributors
  • Lorena Pantano (Bioinformatic Core, Harvard Chan School, Boston, USA)
  • Judith Flo Gaya (School of Engineer and Aplied Science- Harvard University, Boston, USA)
  • Eulalia Marti Puig (Genomics and Disease, Center of Genomic Regulation, Barcelona, Spain)
  • Francisco Pantano Rubino: Architect
  • Steffen Möller (University of Rostock)
Bitdeli badge
About
small RNA analysis from NGS data
seqcluster.readthedocs.io
Topics
mirnareportsequencingsmallrnatrna
Resources
Readme
MIT license
Activity
Stars
39 stars
Watchers
1 watching
Forks
19 forks
Report repository
Releases
Packages
Used by
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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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})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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seqcluster
Ask questions in the repo's Gitter: Join the chat at:
small RNA analysis from NGS data
https://travis-ci.org/lpantano/seqcluster.png?branch=masterhttps://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-squareProject Status: Active - The project has reached a stable, usable state and is being actively developed.https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtv632-lightgrey.svg?style=flat-square
Cite
Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis. Pantano L, Friedländer MR, Escaramís G, Lizano E, Pallarès-Albanell J, Ferrer I, Estivill X, Martí E.
Bioinformatics. 2015 Nov 2. pii: btv632. [Epub ahead of print]
PMID: 26530722
A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.
Pantano L1, Estivill X, Martí E. Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5.
PMID: 21976421
Quick start links
See installation at http://seqcluster.readthedocs.org/installation.html
Moreover bcbio-nextgen provides
a python framework to run a whole pipeline for small RNA (miRNA + tRNA + piRNA + others).
An example of how to run with bcbio is here: http://seqcluster.readthedocs.org/example_pipeline.html#mirqc-data
In case you want to use seqcluster alone, a complete tutorial is here: http://seqcluster.readthedocs.org/getting_started.html#clustering-of-small-rna-sequences
Report
Seqcluster creates html report that looks like this. That is a table of all cluster detected, and you
can go into each of them and get a complete description with profile expression figures, annotation details and
sequences counts for each sample. An interactive report is as well available to explore the expression profile,
position on the genome and secondary structure. Learn more http://seqcluster.readthedocs.org/more_outputs.html#report.
Contributors
  • Lorena Pantano (Bioinformatic Core, Harvard Chan School, Boston, USA)
  • Judith Flo Gaya (School of Engineer and Aplied Science- Harvard University, Boston, USA)
  • Eulalia Marti Puig (Genomics and Disease, Center of Genomic Regulation, Barcelona, Spain)
  • Francisco Pantano Rubino: Architect
  • Steffen Möller (University of Rostock)
Bitdeli badge
About
small RNA analysis from NGS data
seqcluster.readthedocs.io
Topics
mirnareportsequencingsmallrnatrna
Resources
Readme
MIT license
Activity
Stars
39 stars
Watchers
1 watching
Forks
19 forks
Report repository
Releases
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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");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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seqcluster
Ask questions in the repo's Gitter: Join the chat at:
small RNA analysis from NGS data
https://travis-ci.org/lpantano/seqcluster.png?branch=masterhttps://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-squareProject Status: Active - The project has reached a stable, usable state and is being actively developed.https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtv632-lightgrey.svg?style=flat-square
Cite
Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis. Pantano L, Friedländer MR, Escaramís G, Lizano E, Pallarès-Albanell J, Ferrer I, Estivill X, Martí E.
Bioinformatics. 2015 Nov 2. pii: btv632. [Epub ahead of print]
PMID: 26530722
A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.
Pantano L1, Estivill X, Martí E. Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5.
PMID: 21976421
Quick start links
See installation at http://seqcluster.readthedocs.org/installation.html
Moreover bcbio-nextgen provides
a python framework to run a whole pipeline for small RNA (miRNA + tRNA + piRNA + others).
An example of how to run with bcbio is here: http://seqcluster.readthedocs.org/example_pipeline.html#mirqc-data
In case you want to use seqcluster alone, a complete tutorial is here: http://seqcluster.readthedocs.org/getting_started.html#clustering-of-small-rna-sequences
Report
Seqcluster creates html report that looks like this. That is a table of all cluster detected, and you
can go into each of them and get a complete description with profile expression figures, annotation details and
sequences counts for each sample. An interactive report is as well available to explore the expression profile,
position on the genome and secondary structure. Learn more http://seqcluster.readthedocs.org/more_outputs.html#report.
Contributors
  • Lorena Pantano (Bioinformatic Core, Harvard Chan School, Boston, USA)
  • Judith Flo Gaya (School of Engineer and Aplied Science- Harvard University, Boston, USA)
  • Eulalia Marti Puig (Genomics and Disease, Center of Genomic Regulation, Barcelona, Spain)
  • Francisco Pantano Rubino: Architect
  • Steffen Möller (University of Rostock)
Bitdeli badge
About
small RNA analysis from NGS data
seqcluster.readthedocs.io
Topics
mirnareportsequencingsmallrnatrna
Resources
Readme
MIT license
Activity
Stars
39 stars
Watchers
1 watching
Forks
19 forks
Report repository
Releases
Packages
Used by
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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})();
(function(){
try {
var __m = "*";
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seqcluster
Ask questions in the repo's Gitter: Join the chat at:
small RNA analysis from NGS data
https://travis-ci.org/lpantano/seqcluster.png?branch=masterhttps://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-squareProject Status: Active - The project has reached a stable, usable state and is being actively developed.https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtv632-lightgrey.svg?style=flat-square
Cite
Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis. Pantano L, Friedländer MR, Escaramís G, Lizano E, Pallarès-Albanell J, Ferrer I, Estivill X, Martí E.
Bioinformatics. 2015 Nov 2. pii: btv632. [Epub ahead of print]
PMID: 26530722
A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.
Pantano L1, Estivill X, Martí E. Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5.
PMID: 21976421
Quick start links
See installation at http://seqcluster.readthedocs.org/installation.html
Moreover bcbio-nextgen provides
a python framework to run a whole pipeline for small RNA (miRNA + tRNA + piRNA + others).
An example of how to run with bcbio is here: http://seqcluster.readthedocs.org/example_pipeline.html#mirqc-data
In case you want to use seqcluster alone, a complete tutorial is here: http://seqcluster.readthedocs.org/getting_started.html#clustering-of-small-rna-sequences
Report
Seqcluster creates html report that looks like this. That is a table of all cluster detected, and you
can go into each of them and get a complete description with profile expression figures, annotation details and
sequences counts for each sample. An interactive report is as well available to explore the expression profile,
position on the genome and secondary structure. Learn more http://seqcluster.readthedocs.org/more_outputs.html#report.
Contributors
  • Lorena Pantano (Bioinformatic Core, Harvard Chan School, Boston, USA)
  • Judith Flo Gaya (School of Engineer and Aplied Science- Harvard University, Boston, USA)
  • Eulalia Marti Puig (Genomics and Disease, Center of Genomic Regulation, Barcelona, Spain)
  • Francisco Pantano Rubino: Architect
  • Steffen Möller (University of Rostock)
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small RNA analysis from NGS data
seqcluster.readthedocs.io
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seqcluster
Ask questions in the repo's Gitter: Join the chat at:
small RNA analysis from NGS data
https://travis-ci.org/lpantano/seqcluster.png?branch=masterhttps://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-squareProject Status: Active - The project has reached a stable, usable state and is being actively developed.https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtv632-lightgrey.svg?style=flat-square
Cite
Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis. Pantano L, Friedländer MR, Escaramís G, Lizano E, Pallarès-Albanell J, Ferrer I, Estivill X, Martí E.
Bioinformatics. 2015 Nov 2. pii: btv632. [Epub ahead of print]
PMID: 26530722
A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.
Pantano L1, Estivill X, Martí E. Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5.
PMID: 21976421
Quick start links
See installation at http://seqcluster.readthedocs.org/installation.html
Moreover bcbio-nextgen provides
a python framework to run a whole pipeline for small RNA (miRNA + tRNA + piRNA + others).
An example of how to run with bcbio is here: http://seqcluster.readthedocs.org/example_pipeline.html#mirqc-data
In case you want to use seqcluster alone, a complete tutorial is here: http://seqcluster.readthedocs.org/getting_started.html#clustering-of-small-rna-sequences
Report
Seqcluster creates html report that looks like this. That is a table of all cluster detected, and you
can go into each of them and get a complete description with profile expression figures, annotation details and
sequences counts for each sample. An interactive report is as well available to explore the expression profile,
position on the genome and secondary structure. Learn more http://seqcluster.readthedocs.org/more_outputs.html#report.
Contributors
  • Lorena Pantano (Bioinformatic Core, Harvard Chan School, Boston, USA)
  • Judith Flo Gaya (School of Engineer and Aplied Science- Harvard University, Boston, USA)
  • Eulalia Marti Puig (Genomics and Disease, Center of Genomic Regulation, Barcelona, Spain)
  • Francisco Pantano Rubino: Architect
  • Steffen Möller (University of Rostock)
Bitdeli badge
About
small RNA analysis from NGS data
seqcluster.readthedocs.io
Topics
mirnareportsequencingsmallrnatrna
Resources
Readme
MIT license
Activity
Stars
39 stars
Watchers
1 watching
Forks
19 forks
Report repository
Releases
Packages
Used by
Contributors
Languages