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<!-- is generated from README.Rmd. Please edit that file --> # FindIT2:Find influential TF and influential Target <!-- badges: start --> <!-- badges: end --> 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: ``` r 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]( ``` r 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 ``` r 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 ``` r BiocManager::install("shangguandong1996/FindIT2", build_vignettes=TRUE) ``` To view documentation of FindIT2, start R and enter: ``` r browseVignettes("FindIT2") ```