Welcome to the 3D RNA-seq App user group. Any questions, discussions and bug reports are welcome.

Github page of the App: https://github.com/wyguo/ThreeDRNAseq

The ThreeDRNAseq (3D RNA-seq) R package provides an interactive graphical user interface (GUI) for RNA-seq data analysis using accurate quantification of RNA-seq reads. It allows users, even biologists with minor knowledge of bioinformatics, to perform differential expression (DE), differential alternative splicing (DAS) and differential transcript usage (DTU) (3D) analyses based on limma (Ritchie et al., 2015). The 3D RNA-seq GUI is based on R shiny App and enables a complete RNA-seq analysis to be done within only 3 Days (3D). To use our pipeline in your work, please cite:

Guo,W., Tzioutziou,N., Stephen,G., Milne,I., Calixto,C., Waugh,R., Brown,J.W., and Zhang,R. (2019) 3D RNA-seq - a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. bioRxiv, 656686. doi: https://doi.org/10.1101/656686.
Calixto,C.P.G., Guo,W., James,A.B., Tzioutziou,N.A., Entizne,J.C., Panter,P.E., Knight,H., Nimmo,H.G., Zhang,R., and Brown,J.W.S. (2018) Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome. Plant Cell, 30, 1424–1444.

Salmon quant method for input

surbhi grewal