seqcluster 1.1.1

Small RNA-seq pipeline

seqcluster
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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.png?branch=master

.. image:: https://badge.fury.io/py/seqcluster.svg
:target: http://badge.fury.io/py/seqcluster

.. image:: https://pypip.in/d/seqcluster/badge.png
:target: https://pypi.python.org/pypi/seqcluster


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

Moreover `seqcluster-helper`_ provides
a python framework to run a whole pipeline for small RNA (miRNA + tRNA + piRNA + others).

.. _seqcluster-helper: http://seqcluster.readthedocs.org/getting_started.html#easy-start-with-seqcluster-helper-py

Complete tutorial is here: http://seqcluster.readthedocs.org/getting_started.html#clustering-of-small-rna-sequences

report
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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.

.. _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
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* `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)