H3K36me3: ChIP-seq read counts of H3K36me3 from adipose nuclei, bone...

In plbaldoni/mixHMM: Differential Peak Calling via Hidden Markov Model With Mixture of Negative Binomial Distributions

Description

Data from Roadmap Epigenomics Project of H3K36me3 ChIP-seq experiments (3 biological replicates each) from adipose nuclei, bone marrow, and CD34 cells on 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(H3K36me3)

Format

RangedSummarizedExperiment

Source

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM670014 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM669979 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM669997 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM621419 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM670037 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM669996 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM772865 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM706843 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM773042

References

Bernstein, B.E., et al. 2010. The NIH roadmap epigenomics mapping consortium. Nature biotechnology, 28(10), p.1045

Examples

data(H3K36me3)
ChIP = SummarizedExperiment::assay(H3K36me3)

plbaldoni/mixHMM documentation built on Nov. 8, 2019, 8:05 p.m.