.. _Small RNA Tools:


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Tools for downstream analysis
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Web-servers
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`TFmiR`_: disease-specific miRNA/transcription factor co-regulatory networks v1.2. It uses results from UP/DOWN regulated miRNA/Genes and allows to focus in only one disease to create different type of relationships between miRNA/TF/Gene. Easy to use. Probably need to filter the output sometime due to the big networks that can result from an analysis. 

`Diana-TarBase v7.0`_: Database for validated miRNA targets. Many filter options. Good for small candidate miRNAs set studies.

`StarScan`_: Database to browse the targets of miRNAs from degradome data. It has a fancy interface, and many species and data from GEO.

`miRtex <http://research.bioinformatics.udel.edu/miRTex/>`_ gives targets from literature. Good for finding validated targets to help discussion in papers or further functional experiment based on new hypothesis.

`piRBase`_: Database for piRNA annotation and function. Published last year, for now the best I can find out there.

`chimira`_: Web tool to analyze isomiR. It gives you a quick idea of you samples.

`MicroCosm`_: MiRNA target database. Updated and download option.

`IsomiR Bank <http://mcg.ustc.edu.cn/bsc/isomir>`_: isomiR database from many species and tissues. For single queries is useful.

Command-lines
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`miRVaS <http://nar.oxfordjournals.org/content/early/2015/09/17/nar.gkv921.full>`_ : tools to predict the functional changed due to nt changes in the miRNA sequence.


.. _TFmiR: http://service.bioinformatik.uni-saarland.de/tfmir/

.. _Diana-TarBase v7.0: http://diana.imis.athena-innovation.gr/DianaTools

.. _StarScan: http://mirlab.sysu.edu.cn/starscan/Scan.php

.. _piRBase: http://www.regulatoryrna.org/database/piRNA/index.html

.. _chimira: http://wwwdev.ebi.ac.uk/enright-srv/chimira/

.. _MicroCosm: http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/