peaX

peaX is an R data package that provides human transcription factor and histone modification ChIP-seq peaks data from ENCODE and ROADMAP Epigenomics. Files originally downloaded in bigBed format, converted to BED, and then tidied up to include only peak coordinates (chromosome number, peak start position, peak end position) in preparation for large-scale functional annotation.

Data

Currently supported ChIP-seq peak lists in the peaX package include:

1. Proximal, distal, and total peak sets for H3K4me1
2. Proximal, distal, and total peak sets for H3K4me3
3. Proximal, distal, and total peak sets for H3K9ac
4. Proximal, distal, and total peak sets for H3K27ac
5. Proximal, distal, and total peak sets for transcription factors

Installation instructions

You can install the current GitHub version using the devtools package and the following command in R:

if (!require("devtools")) install.packages("devtools")
devtools::install_github("Bohdan-Khomtchouk/peaX")

And then:

library(peaX)