prada to run in linux online online with Winfy

We have hosted the application prada to run in linux online in order to run this application in our online workstations with Wine or directly.

Quick description about prada to run in linux online:

Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification.

PRADA currently supports 7 modules to process and identify abnormalities from RNAseq data:
preprocess: Generates aligned and recalibrated BAM files.
expression: Generates gene expression (RPKM) and quality metrics.
fusion: Identifies candidate gene fusions.
guess-ft: Supervised search for fusion transcripts.
guess-if: Supervised search for intragenic fusions.
homology: Calculates homology between given two genes.
frame: Predicts functional consequence of fusion transcript

Features:

• PRADA is written in python programing language and intended to run in a command line environment on UNIX or LINUX operating systems.
• Detail description of installation steps and the usage of each module with examples is available in the documentation at https: //sourceforge.net/p/prada/wiki/Home/attachment/pyPRADA.pdf
• The hg19 reference files are available to download at http: //bioinformatics.mdanderson.org/Software/PRADA/
• To remove fusion artifacts, we filter out genes with multiple partners in the same sample and homology.

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