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