ChIPseeker is an R package for the analysis and visualization of epigenetics data.
This respository contains R markdown files to be paired with our manuscript "Exploring epigenomic datasets by ChIPseeker" (Current Protocols).
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ChIPseeker_CP_markdown.rmd
Markdown file contains the scripts that are present in the manuscript code windows. Every stage of each protocol is explained in detail.
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ChIPseeker_CP_code.rmd
Markdown file contains the code used to generate the analyses and figures in the manuscript.
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CP_demo_data
This folder contains the example data that is used in this manuscript. The results under NCBI accession numbers GSE52457 and GSE16256 of re-analysed ChIP-seq (H3K4me1, H3K4me3, and CTCF), Methyl-seq, DNase-seq, and smRNA datasets were extracted.