Metadata-Version: 1.1
Name: seqcluster
Version: 1.2.4a15
Summary: Small RNA-seq pipeline
Home-page: http://github.com/lpantano/seqcluster
Author: Lorena Pantano
Author-email: lorena.pantano@gmail.com
License: MIT
Description: seqcluster
        ----------
        
        Ask questions in the repo's Gitter: Join the chat at:
        
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        small RNA analysis from NGS data
        
        .. image:: https://travis-ci.org/lpantano/seqcluster.png?branch=master
           :target: https://travis-ci.org/lpantano/seqcluster
        
        .. image:: https://badge.fury.io/py/seqcluster.svg
           :target: http://badge.fury.io/py/seqcluster
        
        .. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
           :target: http://bioconda.github.io
        
        .. image:: https://anaconda.org/bioconda/seqcluster/badges/downloads.svg
           :target: https://anaconda.org/bioconda/seqcluster
        
        .. image:: https://img.shields.io/pypi/l/seqcluster.svg
           :target: https://github.com/lpantano/seqcluster/blob/master/LICENSE
        
        .. image:: http://www.repostatus.org/badges/latest/active.svg
           :alt: Project Status: Active - The project has reached a stable, usable state and is being actively developed.
           :target: http://www.repostatus.org/#active
        
        .. image:: https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtv632-lightgrey.svg?style=flat-square
           :target: https://doi.org/10.1093/bioinformatics/btv632
        
        Cite
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        **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 <http://www.ncbi.nlm.nih.gov/pubmed/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 <http://www.ncbi.nlm.nih.gov/pubmed/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).
        
        .. _bcbio-nextgen: https://bcbio-nextgen.readthedocs.org/en/latest/
        
        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.
        
        .. _this: https://rawgit.com/lpantano/seqcluster/master/data/examples_report/html/index.html
        .. _description: https://rawgit.com/lpantano/seqcluster/master/data/examples_report/html/1/maps.html
        
        Contributors
        ------------
        
        * `Lorena Pantano  <https://github.com/lpantano>`_ (Bioinformatic Core, Harvard Chan School, Boston, USA)
        * `Judith Flo Gaya <http://www.seas.harvard.edu/directory/jflo>`_ (School of Engineer and Aplied Science- Harvard University, Boston, USA)
        * `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)
        * Francisco Pantano Rubino: Architect
        * `Steffen Möller <https://github.com/smoe>`_ (University of Rostock)
        
        .. image:: https://d2weczhvl823v0.cloudfront.net/lpantano/seqcluster/trend.png
           :alt: Bitdeli badge
           :target: https://bitdeli.com/free
        
Keywords: RNA-seq miRNA snoRNA NGS
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
