README.md

In RiviereQuentin/WimtrapWeb: Plant 'Cis-Acting Regulatory Elements' Prediction Tools

WimtrapWeb

Remark: this is a demo version. The rice will be added soon as well as some improvements of the interface.

WimtrapWeb is a R shiny application for the prediction of condition-specific transcription factor binding sites (TFBS) in plant species. The tool locates the potential TF binding-sites by pattern-matching and annotate them with genomic features that characterize their genomic context (opening of the DNA, chromatin marks, DNA conservation, digital genomic footprints,…). Then, the potential TF binding sites likely to be CARE in the condition of interest are selected based on a ‘decision rules’ model. This model is otained by maching learning using ChIP-seq data as reference.

Prebuilt-models and genomic features integrated into the website allow to quickly obtain prediction of CARE and related potential gene targets in 10 different conditions Arabidopsis thaliana and 2 different conditions for Solanum lycopersicum. Go to the ‘Query’ panel to take advantage of these ressources.

The ‘Build’ and ‘Predict’ panels allow you to build your own models and use them for any other condition and organism.

Installation

WimtrapWeb is an R Shiny Application that requires the last version of R (R 4.0.4), BiocManager and remotes to be installed.

Important: the installation of WimtrapWeb might take up to 1h if all the packages on which it depends need also to be installed.

In R, type the following lines:

    if(!require("remotes", quietly = TRUE)){  
        install.packages("remotes")
        }
    if(!require("BiocManager", quietly = TRUE)){  
        install.packages("BiocManager")
        }

Then, you can enter:

  options(download.file.method = "wininet")
  BiocManager::install("RiviereQuentin/WimtrapWeb",                     
    dependencies = TRUE,                     
    build_vignettes = TRUE,
    force = TRUE)

Example

To start to use WimtrapWeb, please run the app as follows

library(WimtrapWeb)
run_app()
#> PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.

Shiny applications not supported in static R Markdown documents

More informations

Please follow the tutorial video to start using WimtrapWeb:

Methodological details are described in the user guide user guide of the cognate Wimtrap R package and in the manual pages of the functions, which can be accessed by entering in R:

    library(Wimtrap)
    ?importGenomicData()
    ?getTFBSdata()
    ?buildTFBSmodel()
    ?predictTFBS()
    ?plotPredictions()

Authors

This web-application was developed at the LPGMP and MLG groups of the Université Libre de Bruxelles by Quentin Rivière [e-mail], Madalina Ciortan, Massimiliano Corso, Grégoire Noël, Nathalie Verbruggen and Matthieu Defrance [e-mail].

RiviereQuentin/WimtrapWeb documentation built on April 25, 2022, 5:28 a.m.