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genomation: convenience functions for visualing and summarizing genomic intervals

Status Build Status codecov.io BioC_years BioC_availability

This package is a collection of functions for simplfiying common tasks in genomic feature/interval analysis. It provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. It can also annotate given regions with other genomic features such as exons,introns and promoters.

Installation

install via Bioconductor

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("genomation")

Install the latest version via install_github

#' Install dependecies
install.packages( c("data.table","plyr","reshape2","ggplot2","gridBase","devtools"))
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install(c("GenomicRanges","rtracklayer","impute","Rsamtools"))

#' install the packages
library(devtools)
install_github("BIMSBbioinfo/genomation",build_vignettes=FALSE)

Using the package

see the package vignette here