ycl6 / enrichedheatmap-demo

Quick guide to visualize enrichment of genomic signals on targets or regions using EnrichedHeatmap

EnrichedHeatmap Demo

To visualize enrichment of genomic signals on targets or regions using EnrichedHeatmap

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EnrichedHeatmap-Demo web version: https://ycl6.github.io/EnrichedHeatmap-Demo

Package URL: https://github.com/jokergoo/EnrichedHeatmap

Package Doc: http://jokergoo.github.io/EnrichedHeatmap/articles/EnrichedHeatmap.html

Demo Dataset: GSE80779 and GSE80774 from ENL links histone acetylation to oncogenic gene expression in AML. Nature. 2017;543(7644):265-269

License: GPL-3.0

Introduction

In this tutorial, we will use some of the processed data from GSE80779 ChIP-seq and GSE80774 RNA-seq to demonstrate how to use EnrichedHeatmap to show enrichment profiles. In order to build the vignette fast, the data only includes chromosome 22 of human genome (hg19).

Prerequisites

Software & packages

• R version 3.0 and above

This demo requires the following R packages

• data.table from CRAN
• circlize from CRAN
• GenomicRanges from Bioconductor
• EnrichedHeatmap from Bioconductor

Optionally, knitr from CRAN can be used to convert the R Markdown document into an HTML, PDF, or Word document

Demo data used

Data	Type	Description
GSM2136938_MOLM13.H3K27ac	ChIP-seq	Enriched at active enhancers
GSM2136939_MOLM13.H3K4me1	ChIP-seq	Enriched at enhancers (both active and poised)
GSM2136940_MOLM13.H3K4me3	ChIP-seq	Enriched at actively transcribed promoters
GSM2136941_MOLM13.H3K9ac	ChIP-seq	Enriched at active enhancers
GSM2136954_MOLM13.POL2_sgGFP	ChIP-seq	Pol II, Control
GSM2136952_MOLM13.POL2-S2P_sgGFP	ChIP-seq	Pol II Ser2P, Control
GSM2136953_MOLM13.POL2_sgENL5	ChIP-seq	Pol II - ENL KD
GSM2136933_MOLM13.CDK9_Control	ChIP-seq	CDK9, Control
GSM2136934_MOLM13.CDK9_ENLKO	ChIP-seq	CDK9 - ENL KD
GSE80774_MOLM13-sgGFP-DMSO	RNA-seq	Control

Other data used

Data	Description
Gene annotation	From GENCODE v34lift37

Download demo data

Download demo data files from GitHub

cd /ngs/EnrichedHeatmap-Demo

git clone https://github.com/ycl6/EnrichedHeatmap-Demo.git

Go to online tutorial

https://ycl6.github.io/EnrichedHeatmap-Demo/