This is the Windows app named PRADA to run in Windows online over Linux online whose latest release can be downloaded as pyPRADA_1.2.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
Download and run online this app named PRADA to run in Windows online over Linux online with OnWorks for free.
Follow these instructions in order to run this app:
- 1. Downloaded this application in your PC.
- 2. Enter in our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.
- 3. Upload this application in such filemanager.
- 4. Start any OS OnWorks online emulator from this website, but better Windows online emulator.
- 5. From the OnWorks Windows OS you have just started, goto our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.
- 6. Download the application and install it.
- 7. Download Wine from your Linux distributions software repositories. Once installed, you can then double-click the app to run them with Wine. You can also try PlayOnLinux, a fancy interface over Wine that will help you install popular Windows programs and games.
Wine is a way to run Windows software on Linux, but with no Windows required. Wine is an open-source Windows compatibility layer that can run Windows programs directly on any Linux desktop. Essentially, Wine is trying to re-implement enough of Windows from scratch so that it can run all those Windows applications without actually needing Windows.
PRADA to run in Windows online over Linux online
DESCRIPTION:
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.
This is an application that can also be fetched from https://sourceforge.net/projects/prada/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.