E-miR – miRNA analysis and Expression Profiling pipeline

E-miR

:: DESCRIPTION

E-miR is an easy to use perl-based analysis pipeline which was developed to handle the sequencing data in several automated steps including data format conversion, 3′ adapter removal, genome alignment and annotation to non-coding RNA transcripts.

::DEVELOPER

Leiden Genome Technology Center

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux/ MacOsX/ Windows
Perl

:: DOWNLOAD

E-miR

:: MORE INFORMATION

Citation

BMC Genomics. 2010 Dec 20;11:716. doi: 10.1186/1471-2164-11-716.
New methods for next generation sequencing based microRNA expression profiling.
Buermans HP, Ariyurek Y, van Ommen G, den Dunnen JT, ‘t Hoen PA.

miTEA – miRNA Target Enrichment Analysis

miTEA

:: DESCRIPTION

miTEA is a tool for identifying and visualizing enriched miRNA targets in ranked lists of genes.

::DEVELOPER

Laboratory of Computational Biology at the Technion.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

miRNA target enrichment analysis reveals directly active miRNAs in health and disease.
Steinfeld I, Navon R, Ach R, Yakhini Z.
Nucleic Acids Res. 2013 Feb 1;41(3):e45.

miRNA-MATE – A mapping pipeline for SOLiD miRNA data

miRNA-MATE

:: DESCRIPTION

miRNA-MATE is a package designed specifically for mapping and summarizing miRNA (and isomiR) data from SOLiD sequencing data sets. MicroRNAs can be particularly challenging to map because of the limited information content in a 22nt molecule.

::DEVELOPER

Expression Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl
Java

:: DOWNLOAD

miRNA-MATE

:: MORE INFORMATION

Citation

Nicole Cloonan,et al.
MicroRNAs and their isomiRs function cooperatively to target common biological pathways.
Genome Biology 2011, 12:R126