This package implements functions to analyzing multi-omics epigenetic data. Data of fragment type and base type are supported by epiSeeker. It provide function to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among peak data sets, and motif analysis. It incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, overlap of peaks or genes, and the single-base resolution epigenetic data by considering the strand, motif, and additional information.
Guangchuang YU
School of Basic Medical Sciences, Southern Medical University
Get the released version from Bioconductor:
## try http:// if https:// URLs are not supported
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("epiSeeker")Or the development version from github:
## install.packages("devtools")
devtools::install_github("YuLab-SMU/epiSeeker")We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.