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        "description": "seqcluster\n----------\n\nAsk questions in the repo's Gitter: Join the chat at:\n\n.. image:: https://badges.gitter.im/Join%20Chat.svg\n    :target: https://gitter.im/lpantano/seqcluster\n\nsmall RNA analysis from NGS data\n\n.. image:: https://travis-ci.org/lpantano/seqcluster.png?branch=master\n   :target: https://travis-ci.org/lpantano/seqcluster\n\n.. image:: https://badge.fury.io/py/seqcluster.svg\n   :target: http://badge.fury.io/py/seqcluster\n\n.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square\n   :target: http://bioconda.github.io\n\n.. image:: https://anaconda.org/bioconda/seqcluster/badges/downloads.svg\n   :target: https://anaconda.org/bioconda/seqcluster\n\n.. image:: https://img.shields.io/pypi/l/seqcluster.svg\n   :target: https://github.com/lpantano/seqcluster/blob/master/LICENSE\n\n.. image:: http://www.repostatus.org/badges/latest/active.svg\n   :alt: Project Status: Active - The project has reached a stable, usable state and is being actively developed.\n   :target: http://www.repostatus.org/#active\n\n.. image:: https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtv632-lightgrey.svg?style=flat-square\n   :target: https://doi.org/10.1093/bioinformatics/btv632\n\nCite\n---------\n\n**Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis**. Pantano L, Friedl\u00e4nder MR, Escaram\u00eds G, Lizano E, Pallar\u00e8s-Albanell J, Ferrer I, Estivill X, Mart\u00ed E.\nBioinformatics. 2015 Nov 2. pii: btv632. [Epub ahead of print]\nPMID: `26530722 <http://www.ncbi.nlm.nih.gov/pubmed/26530722>`_\n\n**A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.**\nPantano L1, Estivill X, Mart\u00ed E. Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5.\nPMID: `21976421 <http://www.ncbi.nlm.nih.gov/pubmed/21976421>`_\n\nQuick start links\n---------\n\nSee installation at http://seqcluster.readthedocs.org/installation.html\n\nMoreover `bcbio-nextgen`_ provides\na python framework to run a whole pipeline for small RNA (miRNA + tRNA + piRNA + others).\n\n.. _bcbio-nextgen: https://bcbio-nextgen.readthedocs.org/en/latest/\n\nAn example of how to run with bcbio is here: http://seqcluster.readthedocs.org/example_pipeline.html#mirqc-data\n\nIn case you want to use seqcluster alone, a complete tutorial is here: http://seqcluster.readthedocs.org/getting_started.html#clustering-of-small-rna-sequences\n\nReport\n---------\n\nSeqcluster creates html report that looks like `this`_. That is a table of all cluster detected, and you\ncan go into each of them and get a complete `description`_ with profile expression figures, annotation details and\nsequences counts for each sample. An interactive report is as well available to explore the expression profile,\nposition on the genome and secondary structure. Learn more http://seqcluster.readthedocs.org/more_outputs.html#report.\n\n.. _this: https://rawgit.com/lpantano/seqcluster/master/data/examples_report/html/index.html\n.. _description: https://rawgit.com/lpantano/seqcluster/master/data/examples_report/html/1/maps.html\n\nContributors\n------------\n\n* `Lorena Pantano  <https://github.com/lpantano>`_ (Bioinformatic Core, Harvard Chan School, Boston, USA)\n* `Judith Flo Gaya <http://www.seas.harvard.edu/directory/jflo>`_ (School of Engineer and Aplied Science- Harvard University, Boston, USA)\n* `Eulalia Marti Puig <http://www.crg.eu/en/group-members/eul%C3%A0lia-mart%C3%AD-puig>`_ (Genomics and Disease, Center of Genomic Regulation, Barcelona, Spain)\n* Francisco Pantano Rubino: Architect\n* `Steffen M\u00f6ller <https://github.com/smoe>`_ (University of Rostock)\n\n.. image:: https://d2weczhvl823v0.cloudfront.net/lpantano/seqcluster/trend.png\n   :alt: Bitdeli badge\n   :target: https://bitdeli.com/free",
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