Table 1 Major FindIT2 functions

loadPeakFile

read peak file and transform it into GRanges object

mm_nearestGene

annotate peaks using nearest gene mode

mm_geneScan

annotate peaks using gene scan mode

mm_geneBound

search related peaks of interesting genes

plot_annoDistance

plot the distance distribution

peakGeneCor

calculate correlation between gene and peak

enhancerPromoterCor

calculate correlation between enhancer and promoter

getAssocPairNumber

get associated peak number of gene and vice verse

plot_peakGeneAlias_summary

plot the distribution of associated feature number

plot_peakGeneCor

plot correlation between two features

shinyParse_peakGeneCor

explore feature relationship interactively

calcRP_coverage

calculate RP using big wig files

calcRP_region

calculate RP based on mm_geneScan and peak count matrix

calcRP_TFHit

calculate RP based on ChIP-Seq peak data

integrate_ChIP_RNA

integrate ChIP-Seq and RNA-Seq data to find TF target genes

findIT_TTPair

find influential TF of input genes based on public TF-target data

findIT_TFHit

find influential TF of input genes based on public ChIP-seq or motif scan

findIT_enrichFisher

find influential TF of input peaks based on public ChIP-seq or motif scan

findIT_enrichWilcox

find influential TF of input peaks based on public ChIP-seq or motif scan

findIT_regionRP

find influential TF of input genes based on RP and public ChIP-seq or motif scan.

findIT_MARA

infer TF activity based on motif scan and peak count matrix

jaccard_findIT_enrichFisher

calculate jaccard index based on findIT_enrichFisher

jaccard_findIT_TTpair

calculate jaccard index based on findIT_TTPair

integrate_replicates

integrate value from replicates