bioconductor-findit2

name

bioconductor-findit2

description

This package implements functions to find influential TF and target based on different input type. It have 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 function lik

FindIT2

Workflows

Standard Workflow

Annotate ChIP-seq or ATAC-seq peaks to nearest genes and calculate gene-level regulatory potential (RP) based on peak distance to transcription start sites (TSS).

library(FindIT2)
library(TxDb.Athaliana.BioMart.plantsmart28)

# 1. Load peak file and TxDb annotation
Txdb <- TxDb.Athaliana.BioMart.plantsmart28
seqlevels(Txdb) <- c(paste0("Chr", 1:5), "M", "C")
ChIP_peak_path <- system.file(  package  
ChIP_peak_GR  loadPeakFileChIP_peak_path


mmAnno_nearestgene  mm_nearestGenepeak_GR  ChIP_peak_GR Txdb  Txdb


mmAnno_geneScan  mm_geneScanpeak_GR  ChIP_peak_GR Txdb  Txdb upstream   downstream  


fullRP_hit  calcRP_TFHitmmAnno  mmAnno_geneScan Txdb  Txdb decay_dist   report_fullInfo