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.
Package details |
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Author | Wenbin Guo <wenbin.guo@hutton.ac.uk> |
Maintainer | Wenbin Guo <wenbin.guo@hutton.ac.uk> |
License | GPL-3 |
Version | 2.0.1 |
Package repository | View on GitHub |
Installation |
Install the latest version of this package by entering the following in R:
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