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GenomicState

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


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("GenomicState")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
Introduction to GenomicState HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AnnotationData, AnnotationHub, Homo_sapiens, TxDb
Version 0.99.15
License Artistic-2.0
Depends AnnotationHub
Imports GenomicFeatures, GenomeInfoDb, rtracklayer, bumphunter, derfinder(>= 1.21.7), AnnotationDbi, IRanges, org.Hs.eg.db, utils, methods
System Requirements
URL https://github.com/LieberInstitute/GenomicState
Bug Reports https://support.bioconductor.org/t/GenomicState
See More
Suggests knitr, rmarkdown, BiocStyle, sessioninfo, testthat (>= 2.1.0), glue, derfinderPlot, AnnotationHubData, RefManageR, GenomicRanges, covr
Linking To
Enhances
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_0.99.15.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Package Short Url https://bioconductor.org/packages/GenomicState/
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