Huvec: ChIP-seq read counts of H3K36me3 (and input control) from the...

In plbaldoni/ZIMHMM: Improved Detection of Epigenomic Marks With Mixed Effects HMMs

Description

Data from ENCODE project of H3K36me3 (and input control) ChIP-seq experiments (3 replicates each) from Huvec cells of chromosome 19. PCR duplicates were removed with 'samtools markdup'. Low quality reads were removed with 'samtools view -q 10'. The fragment length was estimated using correlateReads and maximizeCcf (from package csaw) after excluding blacklisted positions. Read counts were tabulated using bamCount (from package bamsignals).

Usage

data(Huvec)

Format

RangedSummarizedExperiment

Source

https://www.ncbi.nlm.nih.gov/gds/?term=GSM733757 https://www.ncbi.nlm.nih.gov/gds/?term=GSM733715

References

ENCODE Project Consortium, 2012. An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), p.57.

Examples

data(Huvec)
ChIP = SummarizedExperiment::assay(Huvec,'ChIP')

plbaldoni/ZIMHMM documentation built on Dec. 5, 2019, 11:43 p.m.