MDTToolset

THIS R PACKAGE IS CURRENTLY UNDER DEVELOPMENT

Overview

The R package MDTToolset is designed to calculate the Most Dominant Transcript and their switches in the RNA-Seq datasets. It enables users to:

• Remove redundant transcripts with identical protein sequences and aggregate their transcript counts.
• Calculate the most dominant transcripts in RNA-Seq data using flexible cutoffs, such as user-defined transcript expression and enrichment cutoffs.
• Identify MDTs present in a user-defined percentage of samples.
• Calculate MDT Switching events with flexible user-defined cutoffs.
• Integrate the isoform interaction network with the MDT switches to understand their functional impact on the protein interaction network.
• Visualize the expression of MDTs and disease-specific MDTs (dMDTs).
• Visualize the network of dMDTs.

Background

Alternative splicing plays an essential role in development, tissue specificity and essential cell functions. One gene can encode for many transcripts, one of those transcripts might be expressed at a significantly higher level than the other transcripts. These transcripts are defined as most dominant transcripts (MDTs). In cancer, those canonical MDTs might be switched to other transcripts which we call MDT switching event. The MDTToolset aims to find the MDTs in RNA-seq data and evaluated the MDT switching event in a flexible user-defined way. The user can define cutoffs for the transcript expression, and MDT enrichment.

How to Install

You can install the development version of MDTToolset from GitHub with:

# install.packages("devtools")
devtools::install_github("KarakulakTulay/MDTToolset")

Vignettes

Please find a comprehensive workflow to MDTToolset in the vignette.

Documentation

The HTML documentation of the latest version is available at GitHub.

Credits

The idea behind MDTToolset was developed by Abdullah Kahraman, and the original perl codes for the calculation of MDTs and their switches can be found here.