erma-package {erma} | R Documentation |
Software and data to support epigenomic road map adventures.
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.
VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
data(farhSE) farhSE ee = makeErmaSet() stateProfile(ee[,1:4], symbol="A2M") data(abbCIcols) abbCIcols