This is the Linux app named TVscript whose latest release can be downloaded as tvscript.zip. It can be run online in the free hosting provider OnWorks for workstations.
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TVscript is a tool designed to allow the user to explore the removal of transcripts associated with intra-condition read count variation that is greater than a user specified threshold. A set of updated count files is produced from the original input data in which such transcripts are absent. These updated count files can be subsequently used within downstream analysis, for example, in the identification of differentially expressed transcripts. In the latter, the extent intra-condition variation affects the final lists of identified genes ambiguously, and inconsistently, across different software designed for this task. Being able to explore the effects of removing such variation at varying thresholds increases the intuitive insight relative to both differential expression analysis and to other areas of research that use such data. Full details, and two case studies involving transcriptomic data associated with canid domestication, are available in our paper: link available shortly.
- Exploration of the effects of intra-condition variation across RNA-seq datasets
- Complete test data example within download folder
- Executable jar file, runs on any platform
- Easy to install, just unzip folder
This is an application that can also be fetched from https://sourceforge.net/projects/tvscript/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.