GenomicState

DOI: 10.18129/B9.bioc.GenomicState    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see GenomicState.

Build and access GenomicState objects for use with derfinder tools from sources like Gencode

Bioconductor version: 3.11

This package contains functions for building GenomicState objects from different annotation sources such as Gencode. It also provides access to these files at JHPCE.

Author: Leonardo Collado-Torres [aut, cre]

Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("GenomicState")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GenomicState")

 

HTML	R Script	Introduction to GenomicState
PDF		Reference Manual
Text		NEWS

Details

biocViews	AnnotationData, AnnotationHub, Homo_sapiens, TxDb
Version	0.99.9
License	Artistic-2.0
Depends	AnnotationHub
Imports	GenomicFeatures, GenomeInfoDb, rtracklayer, bumphunter, derfinder, AnnotationDbi, IRanges, org.Hs.eg.db, utils, methods
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, knitcitations, sessioninfo, testthat (>= 2.1.0), glue, derfinderPlot, AnnotationHubData, RefManageR, GenomicRanges
SystemRequirements
Enhances
URL	https://github.com/LieberInstitute/GenomicState
BugReports	https://github.com/LieberInstitute/GenomicState/issues
Depends On Me
Imports Me	brainflowprobes, recountWorkflow
Suggests Me
Links To Me

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GenomicState_0.99.9.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
Package Short Url	https://bioconductor.org/packages/GenomicState/
Package Downloads Report	Download Stats