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R package for genomic feature analysis and visualization
R
branch: master

Merge pull request #95 from katwre/master

BioC check errors improved
latest commit 1010860fbc
@katwre katwre authored

README.md

genomation: convenience functions for visualing and summarizing genomic intervals

This package is a collection of functions for simplfiying common tasks in genomic feature 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

source("http://bioconductor.org/biocLite.R")
biocLite("genomation")

Install the latest version via install_github

#' Install dependecies
install.packages( c("data.table","plyr","reshape2","ggplot2","gridBase","devtools"))
source("http://bioconductor.org/biocLite.R")
biocLite(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

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