FindIT2:Find influential TF and influential Target

FindIT2 is a package that implements functions to find influential TF and target based on different input type.It has five module

• Multi-peak multi-gene annotaion(mmPeakAnno module)
• Calculate regulation potential(calcRP module)
• Find influential Target based on ChIP-Seq and RNA-Seq data(Find influential Target module)
• Find influential TF based on different input(Find influential TF module)
• Calculate peak-gene or peak-peak correlation(peakGeneCor module)

And there are also some other useful functions like integrate different source information, calculate jaccard similarity for your TF. I will introduce all these function in vignettes.

Installation instructions

FindIT2 is available on Bioconductor, you can install it by:

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

BiocManager::install("FindIT2")

For the packages on bioconductor, please make sure you download the latest stable R release from CRAN

If you want the development version, install it directly from GitHub:

BiocManager::install("shangguandong1996/FindIT2")

Document

If you want to download development version and view vignettes using browseVignettes(FindIT2), your R version should be 4.0 or greater according to this issue because I use the BiocStyle to output rmarkdown. Then you have to firstly download the below packages

packages <- c("BiocStyle", "knitr", "rmarkdown", "sessioninfo", "TxDb.Athaliana.BioMart.plantsmart28")
installed_packages <- packages %in% rownames(installed.packages())
if (any(installed_packages == FALSE)) {
    BiocManager::install(packages[!installed_packages])
}

Meanwhile, adding the build_vignettes=TRUE when downloading development version

BiocManager::install("shangguandong1996/FindIT2", build_vignettes=TRUE)

To view documentation of FindIT2, start R and enter:

browseVignettes("FindIT2")