PAIRADISE Server
Table of Contents
How to use this app
This app should be used after running the PAIRADISE pipeline and statistical model. PAIRADISE allows users to view and interact with ASAS events as well as the corresponding sQTL events (if they are available).
Select input data
PAIRADISE allows users to upload their own data or use one of the pre-loaded sets of data (Geuvadis and GM12878):
If uploading your own data, upload one of the two PAIRADISE results files, “pairadise_results_filtered.txt” or “pairadise_results_filtered_FDRxx.txt” (obtained after running our pipeline) to the app. Otherwise, select one of our pre-loaded datasets from the list:
Select an event from the resulting table
Next, select one of the events from the data table that you want to plot. You can sort the data table by Event name, Gene name, SNP name, number of samples, p-values, or minor allele frequency. The data table can also be searched for specific values of any of these attributes.
Enjoy the results!
Once an event is selected, a table displaying several attributes of that event will appear. In addition, the app will also generate a link to view the event in either the Ensembl genome browser or the UCSC genome browser.
The main visualization of the PAIRADISE app is the ASAS plot which will be displayed below the summary table. The ASAS table shows the exon inclusion levels (psi values; horizontal axis) for each of the two alleles and for each sample (vertical axis) of the given event. A pdf or png of the resulting plot can be downloaded by pressing the “Download Plot” button above the plot:
sQTL events
If there is an sQTL event corresponding to the selected ASAS event, it will be displayed in the “sQTL” tab. Otherwise this tab will be empty.
What is PAIRADISE ?
PAIRADISE (PAIred Replicate analysis of Allelic DIfferential Splicing Events) is a method for detecting allele-specific alternative splicing (ASAS) from RNA-seq data. Unlike conventional approaches that detect ASAS events one sample at a time, PAIRADISE aggregates ASAS signals across multiple individuals in a population. By treating the two alleles of an individual as paired, and multiple individuals sharing a heterozygous SNP as replicates, PAIRADISE formulates ASAS detection as a statistical problem for identifying differential alternative splicing from RNA-seq data with paired replicates.
Github
PAIRADISE can be downloaded here. Issues with PAIRADISE or the Shiny app can be reported here.
Contact
Levon Demirdjian levondem@gmail.com
Yi Xing xingyi@email.chop.edu