| 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