POSTRE: Prediction Of STRuctural variant Effects
LATEST UPDATE: 11/09/2024 What is new?
POSTRE can handle now Vision-Eye related phenotypes.
Check the infographic displayed below to see a representation of POSTRE functionality. Click the image to expand it.
POSTRE can be used to analyse Single or Multiple SVs.
Watch POSTRE performance with a real patient in the following YouTube video. Reproduce it in Full Screen and High Quality (1080p) for optimal visualization. For this patient, with BOFS syndrome carrying an inversion (Laugsch et al., 2019), POSTRE successfully predicts the loss of TFAP2A expression in neural crest cells through an enhancer disconnection mechanism.
The Multiple SV Submission box allows the sequential analysis of multiple structural variants (results can be downloaded as txt tables). The SVs may come from just one or multiple patients. The SVs information has to be uploaded in a specific format. The file format consists on 1 line and 7 columns per structural variant. Each structural variant must contain only two breakpoints. The information associated with each column is provided below:
Note: For the case of structural variants happening strictly in one chromosome (deletions, inversions, duplications) the breakpoint 1 is the one associated with a smaller genomic coordinate, and the breakpoint 2 the one associated with a larger genomic coordinate. For translocations, it does not matter.
The data must be stored in a plain text file with column values separated by tabulations
An example file can be found here (to download it: (1) right-click the "Raw" button at the top of the file, (2) select Save Link As…, (3) choose the location on your computer where you want to save the file, and (4) select Save). Additional test files can also be downloaded from the testFiles folder.
Upon the analysis of multiple SVs two main tables are provided. The first one (Results per SV and phenotype) is a table with a pathogenic prediction for each of the SVs and associated phenotypes analyzed. The second one (Results per gene and phenotype) is an aggregation of the pathogenic predictions per gene, phenotype and pathogenic mechanism (coding, long-range). Perform a Multiple SV Submission with one of the test files and check "How to navigate through this page?" section for more details.
A tutorial video showing how to perform and interpret results for a Multiple SV Submission analysis is provided in the following video.
Even though you may not have computational skills, do not be afraid!. POSTRE installation is very easy. On top of that, once POSTRE is installed, running and using it is as simple as any other desktop application. Thanks to its user friendly graphical interface.
POSTRE is built with Shiny framework. Thus, to run POSTRE you only require R (version >=3.5.0).
To run Postre R version >=3.5.0 is required.
There is plenty of available information in the internet about how to install R depending on the OS (Windows, Mac, Linux etc.). Usually upon R installation people also install R-Studio, which is an integrated development environment to write R code. As a result, most tutorials explain how to install both R and R-Studio. But, to run Postre R-Studio is not necessary. If you need help for R download, different tutorials are provided here:
Once R is installed, just execute the following instruction in an R console to run POSTRE latest version:
source("https://raw.githubusercontent.com/vicsanga/Postre/main/Postre_wrapper.R")
The above instruction installs and loads all the required libraries for POSTRE. If some libraries are missing R may ask for permission to install them, confirm it. The first time that you run POSTRE this action will probably take more time.
If you are not sure about how to do it. You can find me initializing POSTRE from R in the video below!
POSTRE can also be uploaded to a server (e.g. shinyapps.io), by a user with R installed, and accessed online as a normal web app by other users.
A detailed explanation on how to do that is provided in Shiny web page.
Recapitulating, you have to:
The advantage of this approach is to provide other users in your organization access to the tool without having R installed. However, the person in charge of uploading POSTRE to the server will have to check for new versions or releases of the tool, and re-upload them to the server when available. Contrarily, if POSTRE is executed from an R terminal, with the source() command given above, in step 2, the latest version of POSTRE will always be executed. If you want to be notified when new major releases of the tool are available, please, send a mail to postre.radaiglesiaslab@gmail.com to be added to the notifications mail list.
If you want to use POSTRE as an R function, and not through its graphical user interface, you can do that by following the steps provided below. Importantly, if you want to take profit of POSTRE latest version, to update POSTRE R function you will have to repeat the steps 1 and 2 each time a new version is released. Latest version release date: 11/09/2024. If you want to be notified when new major releases of the tool are available, please, send a mail to postre.radaiglesiaslab@gmail.com to be added to the notifications mail list.
Steps for using POSTRE as an R function:
If you are experiencing some trouble, or you just want to contact us for any reason, please send a mail to postre.radaiglesiaslab@gmail.com.