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rje_miRNA V0.3

Miscellaneous miRNA Analysis Module

Module: rje_miRNA
Description: Miscellaneous miRNA Analysis Module
Version: 0.3
Last Edit: 15/07/13

Copyright © 2008 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_db rje_seq rje_slim rje_zen slimfinder


See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module controls various custom miRNA analyses. It is envisioned that it will be replaced in time with other modules.

Commandline

INPUT

seqin=FILE : Main file for analysis, containing UTRs []
maxseq=X : Maximum number of sequences to process [500]
seedfreq=T/F: Whether to use overall Seed Frequencies per sequence for slimprob [False]

ANALYSIS

run=LIST : List of analyses/manipulations (nrutr/enspita/cleal) []
enspath=PATH: Path to EnsLoci files [/scratch/Databases/NewDB/EnsEMBL/]

CLEAL Analysis

minmax=X : Minimum value for Maximum expression value [1.0]
arraydata=FILE : File of array data for Cleal analysis []
miranda=FILE : Miranda prediction file []
validated=FILE : Validate mRNA target file []

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - Shifted focus of analysis to use PITA instead.
    # 0.2 - Added Cleal Analysis of Placental versus miRanda downloads (http://www.microrna.org/microrna/getDownloads.do)
    # 0.3 - Tidied up some import calls.

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.