In aryeelab/diffloopdata: Example ChIA-PET Datasets for the diffloop Package

The diffloopdata package contains an example dataset for use with the diffloop package.

It contains chromosome 1 data from 6 ChIA-PET samples.$^{1,2}$ The raw FASTQ read files were preprocessed with the dnaloop (https://github.com/aryeelab/dnaloop) package. These six samples were ChIP'd against the SMC1 protein, a subunit of cohesin. Additionally, 5 samples against the POL2 protein are included from the K562, MCF7, and HCT116 cell lines. Processed RNA-Seq counts for the K562 and MCF7 cell lines are the last component of the package, which were aligned using bowtie then mapped to Refseq hg19 genes using HT-Seq. Additional data to utilize the wealth of functions in diffloop include processed data from the 450k DNA methylation array, CNV regions, and H3K27ac peaks.These data were all available through the ENCODE Project.

$^1$Hnisz, Denes, et al. "Activation of proto-oncogenes by disruption of chromosome neighborhoods." Science (2016): aad9024.

$^2$Ji, Xiong, et al. "3D Chromosome Regulatory Landscape of Human Pluripotent Cells." Cell stem cell (2015).

aryeelab/diffloopdata documentation built on May 12, 2019, 3:43 a.m.