erma-package {erma}R Documentation

epigenomic road map adventures

Description

Software and data to support epigenomic road map adventures.

Details

The DESCRIPTION file:

Package: erma
Title: epigenomic road map adventures
Version: 1.3.0
Author: VJ Carey <stvjc@channing.harvard.edu>
Description: Software and data to support epigenomic road map adventures.
Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel
Depends: R (>= 3.1), methods, Homo.sapiens, GenomicFiles (>= 1.5.2)
Imports: rtracklayer (>= 1.38.1), S4Vectors (>= 0.23.18), BiocGenerics, GenomicRanges, SummarizedExperiment, ggplot2, GenomeInfoDb, Biobase, shiny, BiocParallel, IRanges, AnnotationDbi
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
License: Artistic-2.0
LazyLoad: yes
BiocViews: Epigenetics, panomics, Annotation, ChIPSeq
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/erma
git_branch: master
git_last_commit: 50b27b8
git_last_commit_date: 2019-10-29
Date/Publication: 2019-11-10

Index of help topics:

ErmaSet-class           Class '"ErmaSet"'
erma-package            epigenomic road map adventures
genemodel               create GRanges instance with model for a gene
mapmeta                 create a DataFrame instance providing metadata
                        about the Epigenomics Roadmap
stateProfile            create a ggplot2 visualization of chromatin
                        states over genomic addresses for a family of
                        cell types managed in an ErmaSet instance
states_25               metadata on states of 25-state model of
                        chromatin from ChromImpute, and on cell types
                        in the epigenome road map of April 2015

This package provides infrastructure for working with products of the NIH epigenome roadmap project.

Author(s)

VJ Carey <stvjc@channing.harvard.edu>

Maintainer: VJ Carey <stvjc@channing.harvard.edu>

Examples

data(farhSE)
farhSE
ee = makeErmaSet()
stateProfile(ee[,1:4], symbol="A2M")
data(abbCIcols)
abbCIcols

[Package erma version 1.3.0 Index]