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.. _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/
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