README.md

In RiviereQuentin/Wimtrap: Integrative tools to predict the location of transcription factor binding sites

Wimtrap

Wimtrap: Integrative tools to predict the location of transcription factor binding sites

Installation

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

Important: the installation of Wimtrap 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(repos = BiocManager::repositories()) getOption("repos") BiocManager::install("RiviereQuentin/Wimtrap", dependencies = TRUE, build_vignettes = TRUE, force = TRUE) ````

If an error occurs, it might be because the version of R, BiocManager and/or remotes is not updated.

In some cases, we also noticed that it might be necessary to install beforehand the dependence e1071:

  if(!require("e1071", quietly = TRUE)){  
    install.packages("e1071")
    }
  BiocManager::install("RiviereQuentin/Wimtrap",                     
    dependencies = TRUE,                     
    build_vignettes = TRUE)

On linux, it might be also necessary to install as a prerequisite some software. On ubuntu, this might be achieved by entering the following in the terminal:

sudo apt install libcurl4-gnutls-dev icu-devtools libicu-dev libxml2-dev bzip2-doc libbz2-dev liblzma-dev

Predictions of transcription factor binding sites in Arabidopsis thaliana or Solanum lycopersicum

Pre-built models are available for Arabidopsis and the tomato.

Predictions can be made taking into consideration chromatin state features related to different conditions (for Arabidopsis: whole seedlings, seedling roots, non-hair part of seedling roots, flowers in stages 4-5, seed coats, heat-shocked seedlings, dark-grown seedlings, dark-grown seedlings exposed to 30min or 3h of light and dark-grown seedlings exposed to a long-day cycle; for the tomato: immature and ripening fruits).

To predict the binding sites of "AT2G46830" in flowers of Arabidopsis or of "Solyc00g0224680.1" in immature fruits of tomato, type:

    library(Wimtrap)
    #Predictions of the binding sites of "AT2G46830" in flowers of Arabidopsis
    CCA1predictions.flowers <- carepat(organism = "Arabidopsis thaliana",
                                       condition = "flowers",
                                       TFnames = "AT2G46830")
    #Predictions of the binding sites of "Solyc00g024680.1" in immature fruits of tomato
    DOF24predictions.immature <- carepat(organism = "Solanum lycopersicum",
                                         condition = "immature_fruits",
                                         TFnames = "Solyc00g024680.1")

Build and apply a predictive model

Extensive details about the functionalities offered by Wimtrap are provide in the user guide and in the manual pages of the functions, which can be accessed by entering in R:

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

RiviereQuentin/Wimtrap documentation built on June 29, 2024, 7:17 p.m.