wyguo/ThreeDRNAseq: 3D RNA-seq App enables RNA-seq data analysis to be done only within 3 Days.

This package provides an interactive graphical user interface (GUI) for RNA-seq data differential expression (DE), differential alternative splicing (DAS) and differential transcript usage (DTU) analyses based on two popular pipelines: limma and edgeR. The 3D RNA-seq GUI is based on R shiny App and enables command-line-free analysis. To perform analysis, the first step is to generate transcript quantification from quantification tools, such as Salmon and Kallisto (1-2 Days). Then users can do mouse click on the App to upload transcript read counts, perform DE and DAS analysis, and make beautiful plots, e.g. expression mean-variance trend plots, PCA plots, heatmap, GO annotation plots, etc. (1 Day or less). The pipeline has steps of proper data pre-processing and false positive controls. These lead to robust 3D predictions. All the results and plots can be saved to a report in html, pdf or word format. The analysis pipeline has been successfully used in different RNA-seq studies from Arabidopsis, barley and potato.

install.packages("remotes")
remotes::install_github("wyguo/ThreeDRNAseq")